NCBI Conserved Domain Search

RNA recognition motif;

279-347

8.09e-12

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 60.69 E-value: 8.09e-12

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002231664  279 TLLVSNLNTDkIDEDKLFNLFSMYGNIVRIKILKNKPDH-----ALIQMADGLQAELAVLYLKGAMLFGKKLEV 347
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLVRDKETGkskgfAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Name

Accession

Description

Interval

E-value

hnRNP-L_PTB

TIGR01649

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...

4-460

4.57e-125

Pssm-ID: 273733 [Multi-domain] Cd Length: 481 Bit Score: 372.23 E-value: 4.57e-125

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQEL 83
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664  84 TTDQSShgrNPDQEEPNRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGR 163
Cdd:TIGR01649  81 KRDGNS---DFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 164 NIYDGCCQLDIQYSNLSELQVHYNNDRSRDFTNPSLP------TEQRSRSSQPS--YNDPSSlFGFQQPGDPYAQVSmDI 235
Cdd:TIGR01649 158 DIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPgrrdpgLDQTHRQRQPAllGQHPSS-YGHDGYSSHGGPLA-PL 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 236 SYKASAALCYFNISPYqmsKAAMIAAAFGGTLP-PGVSGINDRCTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNK 314
Cdd:TIGR01649 236 AGGDRMGPPHGPPSRY---RPAYEAAPLAPAISsYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 315 PDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKYPTV----TADPDA-----RDYSTSHLNRFNSNVVKNYRHCCA 385
Cdd:TIGR01649 313 KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVqpprEGQLDDgltsyKDYSSSRNHRFKKPGSANKNNIQP 392

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 386 PTKMIHISALPQDITEDTIHSLVGEHGTIANS--RLFETNGKTQ--ALVLFESVEEATEALVEKHASKLDRTN------I 455
Cdd:TIGR01649 393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKkfKFFPKDNERSkmGLLEWESVEDAVEALIALNHHQLNEPNgsapyhL 472


                  ....*
gi 1002231664 456 RISFS 460
Cdd:TIGR01649 473 KVSFS 477

RRM2_PTBPH3

cd12692

RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 3 ...

99-186

8.83e-53

Pssm-ID: 410092 [Multi-domain] Cd Length: 88 Bit Score: 172.43 E-value: 8.83e-53

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664  99 PNRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSN 178
Cdd:cd12692     1 PNRILLVTIHHPLYPITVDVLHQVFSPHGFVEKIVTFQKSAGLQALIQYQSQQSAVQARSALQGRNIYDGCCQLDIQFSN 80


                  ....*...
gi 1002231664 179 LSELQVHY 186
Cdd:cd12692    81 LQELQVNY 88

RRM3_PTBPH3

cd12698

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 ...

277-352

2.40e-42

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subgroup corresponds to the RRM3 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410098 [Multi-domain] Cd Length: 76 Bit Score: 144.42 E-value: 2.40e-42

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 277 RCTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKY 352
Cdd:cd12698     1 TPVLLVSNLNPEKVDVDKLFNLFSLYGNIVRIKILRNKPDHALIQMSDPFQAELAVNYLKGAMLFGKSLEVNFSKH 76

RRM2_PTBP1_hnRNPL_like

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

102-186

8.50e-41

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.

Pssm-ID: 409856 [Multi-domain] Cd Length: 85 Bit Score: 140.79 E-value: 8.50e-41

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNLSE 181
Cdd:cd12422     1 VLLVTVTNLLYPVTVDVLHQVFSPYGAVEKIVIFEKGTGVQALVQFDSVESAEAAKKALNGRNIYDGCCTLDIQFSRLKE 80


                  ....*
gi 1002231664 182 LQVHY 186
Cdd:cd12422    81 LTVKY 85

RRM2_PTBP1_like

cd12693

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

100-195

6.62e-39

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410093 [Multi-domain] Cd Length: 96 Bit Score: 135.94 E-value: 6.62e-39

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 100 NRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNL 179
Cdd:cd12693     1 NPVLRVIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALIQFADAVSAQAAKLSLDGQNIYNGCCTLRIDFSKL 80

                          90
                  ....*....|....*.
gi 1002231664 180 SELQVHYNNDRSRDFT 195
Cdd:cd12693    81 TSLNVKYNNDKSRDYT 96

RRM1_PTBPH3

cd12687

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...

6-80

7.77e-38

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410088 [Multi-domain] Cd Length: 75 Bit Score: 132.69 E-value: 7.77e-38

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002231664   6 KVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSH 80
Cdd:cd12687     1 KVLHVRNVGHEISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYIQFSSH 75

RRM4_PTBPH3

cd12426

RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 ...

381-459

1.38e-35

RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 409860 [Multi-domain] Cd Length: 79 Bit Score: 126.55 E-value: 1.38e-35

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 381 RHCCAPTKMIHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATEALVEKHASKLDRTNIRISF 459
Cdd:cd12426     1 RYCCSPTKMIHVSSLPQDVTEEDVLNHLQEHGAIVNTKVFESNGKKQALVLFENEEQATEALVCKHASSLGGSTIRISF 79

RRM_5

pfam13893

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

266-367

1.10e-31

Pssm-ID: 433561 [Multi-domain] Cd Length: 125 Bit Score: 117.59 E-value: 1.10e-31

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 266 TLPPGVSGINDRCTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKL 345
Cdd:pfam13893  15 TGWPGAAGVAGNSVLMVYGLNPDRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRAIQHLNGHPLFGKRL 94

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1002231664 346 EVNYSKYPTVTA---------DPDARDYSTS 367
Cdd:pfam13893  95 QIILSKQQAVSYalpfelqddSPSFKDYSNS 125

RRM1_PTBP1_hnRNPL_like

cd12421

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

7-80

1.24e-31

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.

Pssm-ID: 409855 [Multi-domain] Cd Length: 74 Bit Score: 115.75 E-value: 1.24e-31

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002231664   7 VIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSH 80
Cdd:cd12421     1 VVHIRNLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPVYVQYSNH 74

RRM3_hnRNPL_like

cd12424

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...

280-352

9.73e-30

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs.

Pssm-ID: 409858 [Multi-domain] Cd Length: 74 Bit Score: 110.78 E-value: 9.73e-30

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 280 LLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKY 352
Cdd:cd12424     2 LMVYGLDPDKMNCDRLFNLLCLYGNVLKIKFLKSKPGTAMVQMGDPVAADRAIQNLNNVVLFGQKLQLTYSKQ 74

RRM2_PTBP1

cd12782

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...

102-201

3.48e-29

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM2 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

Pssm-ID: 410174 [Multi-domain] Cd Length: 108 Bit Score: 110.57 E-value: 3.48e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNLSE 181
Cdd:cd12782     7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 86

                          90       100
                  ....*....|....*....|
gi 1002231664 182 LQVHYNNDRSRDFTNPSLPT 201
Cdd:cd12782    87 LNVKYNNDKSRDYTRPDLPS 106

RRM3_PTBPH1_PTBPH2

cd12690

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 1 ...

102-195

3.74e-29

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM3 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410091 [Multi-domain] Cd Length: 97 Bit Score: 109.96 E-value: 3.74e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYD-GCCQLDIQYSNLS 180
Cdd:cd12690     3 VLLASIENMQYAVTLDVLHTVFSAFGFVQKIAIFEKNGGFQALIQYPDVPTAVVAKEALEGHCIYDgGYCKLHLSYSRHT 82

                          90
                  ....*....|....*
gi 1002231664 181 ELQVHYNNDRSRDFT 195
Cdd:cd12690    83 DLNVKVNNDRSRDYT 97

RRM2_ROD1

cd12784

RNA recognition motif 2 (RRM2) found in vertebrate regulator of differentiation 1 (Rod1); This ...

102-201

1.14e-28

RNA recognition motif 2 (RRM2) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM2 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.

Pssm-ID: 410176 [Multi-domain] Cd Length: 108 Bit Score: 108.94 E-value: 1.14e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNLSE 181
Cdd:cd12784     5 VLRIIVENLFYPVTLEVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPMNAHHAKVALDGQNIYNACCTLRIEFSKLTS 84

                          90       100
                  ....*....|....*....|
gi 1002231664 182 LQVHYNNDRSRDFTNPSLPT 201
Cdd:cd12784    85 LNVKYNNDKSRDFTRLDLPS 104

RRM2_PTBP2

cd12783

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 2 ...

102-201

2.23e-28

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM2 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410175 [Multi-domain] Cd Length: 107 Bit Score: 108.17 E-value: 2.23e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNLSE 181
Cdd:cd12783     3 VLRIIIDNMYYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFSKLVN 82

                          90       100
                  ....*....|....*....|
gi 1002231664 182 LQVHYNNDRSRDFTNPSLPT 201
Cdd:cd12783    83 LNVKYNNDKSRDYTRPDLPS 102

RRM3_PTBP1_like

cd12423

RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

280-352

1.54e-25

RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 409857 [Multi-domain] Cd Length: 74 Bit Score: 99.23 E-value: 1.54e-25

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 280 LLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKY 352
Cdd:cd12423     2 LLVSNLNEEMVTPDALFTLFGVYGDVLRVKILFNKKDTALIQMADPQQAQTALQHLNGIKLFGKPIRVTLSKH 74

RRM1_ROD1

cd12779

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...

4-86

3.26e-25

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM1 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.

Pssm-ID: 410171 [Multi-domain] Cd Length: 90 Bit Score: 98.94 E-value: 3.26e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQEL 83
Cdd:cd12779     4 PSRVLHIRKIPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNYYTTVTPHLRNQPVYIQYSNHREL 83


                  ...
gi 1002231664  84 TTD 86
Cdd:cd12779    84 KTD 86

RRM2_hnRNPL_like

cd12694

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...

100-185

2.84e-24

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410094 [Multi-domain] Cd Length: 86 Bit Score: 96.19 E-value: 2.84e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 100 NRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSaGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNL 179
Cdd:cd12694     1 NHVLLFTILNPLYPITVDVIHTICSPYGKVLRIVIFRKN-GVQAMVEFDSVESAQRAKAALNGADIYSGCCTLKIEYAKP 79


                  ....*.
gi 1002231664 180 SELQVH 185
Cdd:cd12694    80 TRLNVY 85

RRM1_PTBP1

cd12777

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...

6-86

3.02e-22

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM1 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

Pssm-ID: 410169 [Multi-domain] Cd Length: 81 Bit Score: 90.42 E-value: 3.02e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   6 KVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQELTT 85
Cdd:cd12777     1 RVIHVRKLPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT 80


                  .
gi 1002231664  86 D 86
Cdd:cd12777    81 D 81

RRM1_PTBP2

cd12778

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...

5-86

7.84e-22

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM1 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410170 [Multi-domain] Cd Length: 82 Bit Score: 89.35 E-value: 7.84e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   5 SKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQELT 84
Cdd:cd12778     1 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYTAVTPHLRNQPIYIQYSNHKELK 80


                  ..
gi 1002231664  85 TD 86
Cdd:cd12778    81 TD 82

RRM1_PTBP1_like

cd12688

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

6-86

4.93e-21

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM1 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and functions at several aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410089 [Multi-domain] Cd Length: 81 Bit Score: 86.98 E-value: 4.93e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   6 KVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQELTT 85
Cdd:cd12688     1 RVLHIRKLPCDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYIQYSNHKELKT 80


                  .
gi 1002231664  86 D 86
Cdd:cd12688    81 D 81

RRM2_hnRPLL

cd12786

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein ...

100-195

6.78e-21

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM2 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 241230 [Multi-domain] Cd Length: 96 Bit Score: 86.99 E-value: 6.78e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 100 NRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSaGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNL 179
Cdd:cd12786     2 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARP 80

                          90
                  ....*....|....*.
gi 1002231664 180 SELQVHYNNDRSRDFT 195
Cdd:cd12786    81 TRLNVIRNDNDSWDYT 96

RRM_8

pfam11835

RRM-like domain; This domain is related to the RRM domains suggesting it may have an ...

102-177

1.08e-20

RRM-like domain; This domain is related to the RRM domains suggesting it may have an RNA-binding function.

Pssm-ID: 432114 Cd Length: 89 Bit Score: 86.36 E-value: 1.08e-20

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 102 ILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYS 177
Cdd:pfam11835  12 VLRVTVSHILYPVTSEVLHQVYDTYGAVAVQVLAVSTWHVEALVSFMSSCDAERARSATHGRNIYDGGCLLDVQHA 87

RRM3_PTBP1

cd12695

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...

280-355

1.23e-20

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

Pssm-ID: 410095 [Multi-domain] Cd Length: 93 Bit Score: 86.21 E-value: 1.23e-20

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 280 LLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKYPTV 355
Cdd:cd12695     2 LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPIRITLSKHQTV 77

RRM2_hnRNPL

cd12785

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...

100-197

4.79e-20

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM2 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both hnRNP-L and PTB are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410177 [Multi-domain] Cd Length: 100 Bit Score: 84.72 E-value: 4.79e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 100 NRILLVTIHHMLYPITIEVLHQVFSPYGFVEKIVTFQKSaGFQTLIQYQSRQSAIQAYGALHGRNIYDGCCQLDIQYSNL 179
Cdd:cd12785     4 NNVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKN-GVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKP 82

                          90
                  ....*....|....*...
gi 1002231664 180 SELQVHYNNDRSRDFTNP 197
Cdd:cd12785    83 TRLNVFKNDQDTWDYTNP 100

RRM3_PTBP2

cd12696

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 ...

269-355

1.60e-18

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410096 [Multi-domain] Cd Length: 107 Bit Score: 80.81 E-value: 1.60e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 269 PGVSGINDRcTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVN 348
Cdd:cd12696     6 PGVSAGGNT-VLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRVT 84


                  ....*..
gi 1002231664 349 YSKYPTV 355
Cdd:cd12696    85 LSKHQTV 91

RRM1_PTBPH1_PTBPH2

cd12686

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 ...

4-79

1.42e-17

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410087 [Multi-domain] Cd Length: 81 Bit Score: 77.16 E-value: 1.42e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTVA--KLVMLRAKNQALVQMEDLASAVNVIQYY--NTIQPSVRGRNVYLQYSS 79
Cdd:cd12686     1 PSKVLHLRNLPWECTEEELIELCKPFGTVVntKCNVGANKNQAFVEFADLNQAISMVSYYasSSEPAQVRGKTVYLQYSN 80

RRM3_ROD1

cd12697

RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This ...

280-352

2.66e-17

RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.

Pssm-ID: 410097 [Multi-domain] Cd Length: 76 Bit Score: 76.16 E-value: 2.66e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 280 LLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSKY 352
Cdd:cd12697     3 LLVSNLNPDAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLYGKVLRATLSKH 75

RRM2_PTBPH1_PTBPH2

cd12691

RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 1 ...

102-186

4.81e-17

RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM2 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 241135 [Multi-domain] Cd Length: 95 Bit Score: 76.04 E-value: 4.81e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 102 ILLVTIHHM-LYPITIEVLHQVFSPYGFVEKIVTFQKSAGFQTLIQYQSRQSAIQAYGALHGRNI-------YDGCCQLD 173
Cdd:cd12691     3 VLLVTIEGVeAGDVSIDVLHLVFSAFGFVHKIATFEKTAGFQALVQFTDAETASAARSALDGRSIpryllpeHVGPCSLR 82

                          90
                  ....*....|...
gi 1002231664 174 IQYSNLSELQVHY 186
Cdd:cd12691    83 ISYSAHTDLNVKF 95

RRM1_hnRNPL_like

cd12689

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...

4-83

8.69e-16

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410090 [Multi-domain] Cd Length: 80 Bit Score: 71.92 E-value: 8.69e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQEL 83
Cdd:cd12689     1 PSPVVHVRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPAYFNYSTSQKI 80

RRM3_hnRNPL

cd12699

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...

276-351

2.70e-15

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM3 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology with polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410099 [Multi-domain] Cd Length: 77 Bit Score: 70.72 E-value: 2.70e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 276 DRCTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSK 351
Cdd:cd12699     1 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKLNVCVSK 76

RRM3_hnRPLL

cd12700

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein ...

281-351

4.01e-13

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM3 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410100 [Multi-domain] Cd Length: 74 Bit Score: 64.27 E-value: 4.01e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 281 LVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSK 351
Cdd:cd12700     3 MVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSK 73

RRM1_2_MATR3_like

cd12436

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...

6-78

3.34e-12

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.

Pssm-ID: 409870 [Multi-domain] Cd Length: 76 Bit Score: 61.98 E-value: 3.34e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002231664   6 KVIHIRNVGH-EISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYS 78
Cdd:cd12436     1 RVLYLTGLPVsKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVS 74

RRM_SF

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

280-348

6.16e-12

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 60.76 E-value: 6.16e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 280 LLVSNLNTDkIDEDKLFNLFSMYGNIVRIKILKNKPDH----ALIQMADGLQAELAVLYLKGAMLFGKKLEVN 348
Cdd:cd00590     1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIVRDRDGKskgfAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RRM

RNA recognition motif;

279-347

8.09e-12

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 60.69 E-value: 8.09e-12

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002231664  279 TLLVSNLNTDkIDEDKLFNLFSMYGNIVRIKILKNKPDH-----ALIQMADGLQAELAVLYLKGAMLFGKKLEV 347
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLVRDKETGkskgfAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RRM1_hnRNPL

cd12780

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...

4-83

9.32e-12

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM1 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410172 [Multi-domain] Cd Length: 80 Bit Score: 60.64 E-value: 9.32e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQEL 83
Cdd:cd12780     1 PSPVVHIRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQALVEFEDILGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 80

RRM4_PTBP1_like

cd12425

RNA recognition motif 4 (RRM4) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

391-460

7.86e-10

RNA recognition motif 4 (RRM4) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 409859 [Multi-domain] Cd Length: 76 Bit Score: 54.97 E-value: 7.86e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002231664 391 HISALPQDITEDTIHSL-VGEHGTIANSRLFETNGKtQALVLFESVEEATEALVEKHASKLDRTN-IRISFS 460
Cdd:cd12425     3 HLSNIPPSVTEEDLKDLfTSTGGTVKAFKFFQKDRK-MALIQMGSVEEAIEALIALHNYQLSENShLRVSFS 73

RRM1_hnRPLL

cd12781

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein ...

5-84

3.19e-09

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); This subgroup corresponds to the RRM1 of hnRNP-LL, which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410173 [Multi-domain] Cd Length: 84 Bit Score: 53.50 E-value: 3.19e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664   5 SKVIHIRNVGHEISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSHQELT 84
Cdd:cd12781     3 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENVESAKKCVTFAADEPVYIAGQQAFFNYSTSKRIT 82

RRM1_U1A_like

cd12246

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...

279-351

1.07e-08

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.

Pssm-ID: 409692 [Multi-domain] Cd Length: 78 Bit Score: 51.77 E-value: 1.07e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 279 TLLVSNLNtDKIDEDK----LFNLFSMYGNIVRIKILKNKPD--HALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSK 351
Cdd:cd12246     1 TLYINNLN-EKIKKDElkrsLYALFSQFGPVLDIVASKSLKMrgQAFVVFKDVESATNALRALQGFPFYGKPMRIQYAK 78

RRM4_ROD1

cd12703

RNA recognition motif 4 (RRM4) found in vertebrate regulator of differentiation 1 (Rod1); This ...

378-461

2.21e-08

RNA recognition motif 4 (RRM4) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM4 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.

Pssm-ID: 410102 [Multi-domain] Cd Length: 91 Bit Score: 51.61 E-value: 2.21e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 378 KNYRHCCAPTKMIHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATEALVEKHASKL-DRTNIR 456
Cdd:cd12703     4 KNFQNIFPPSATLHLSNIPPSVTDDDLKRLFASTGCSVKAFKFFQKDRKMALIQLGSVEEAIQALIELHNHDLgENHHLR 83


                  ....*
gi 1002231664 457 ISFSQ 461
Cdd:cd12703    84 VSFSK 88

RRM_hnRNPC_like

cd12341

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...

278-348

4.82e-08

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.

Pssm-ID: 409778 [Multi-domain] Cd Length: 68 Bit Score: 49.55 E-value: 4.82e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 278 CTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNkpdHALIQMADGLQAELAVLYLKGAMLFGKKLEVN 348
Cdd:cd12341     1 SRIFVGNLPTDQMTKEDLEEIFSKYGKILGISLHKG---YGFVQFDNEEDARAAVAGENGRTIKGQRLDIN 68

RRM_SF

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

390-458

1.26e-07

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 48.82 E-value: 1.26e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002231664 390 IHISALPQDITEDTIHSLVGEHGTIANSRLFETNG---KTQALVLFESVEEATEALVEKHASKLDRTNIRIS 458
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RRM2_PTBP1_hnRNPL_like

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

392-465

1.26e-07

Pssm-ID: 409856 [Multi-domain] Cd Length: 85 Bit Score: 49.11 E-value: 1.26e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 392 ISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATEALvekhaSKLDRTNI-------RISFSQMQN 464
Cdd:cd12422     6 VTNLLYPVTVDVLHQVFSPYGAVEKIVIFEKGTGVQALVQFDSVESAEAAK-----KALNGRNIydgcctlDIQFSRLKE 80


                  .
gi 1002231664 465 I 465
Cdd:cd12422    81 L 81

RRM2_MATR3

cd12715

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...

6-75

2.43e-07

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.

Pssm-ID: 410114 [Multi-domain] Cd Length: 80 Bit Score: 48.29 E-value: 2.43e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664   6 KVIHIRNVGHE-ISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGR--NVYL 75
Cdd:cd12715     1 RVIHLSNLPHSgYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRcvKVDL 73

RRM

RNA recognition motif;

7-75

3.54e-07

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 47.59 E-value: 3.54e-07

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002231664    7 VIHIRNVGHEISESELLQVVQPFGTVAKLVMLR------AKNQALVQMEDLASAVNVIQYYNTIQpsVRGRNVYL 75
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdketgkSKGFAFVEFESEEDAEKALEALNGKE--LDGRPLKV 73

RRM1_p54nrb_like

cd12332

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...

277-349

4.83e-07

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.

Pssm-ID: 409769 [Multi-domain] Cd Length: 71 Bit Score: 46.91 E-value: 4.83e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 277 RCTLLVSNLNTDkIDEDKLFNLFSMYGNIVRIKILKNKpDHALIQMADGLQAELAVLYLKGAMLFGKKLEVNY 349
Cdd:cd12332     1 RCRLFVGNLPND-ITEEEFKELFQKYGEVSEVFLNKGK-GFGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71

RRM_SF

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

8-76

1.02e-06

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 46.12 E-value: 1.02e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002231664   8 IHIRNVGHEISESELLQVVQPFGTVAKLVMLRA-----KNQALVQMEDLASAVNVIQYYNTIQpsVRGRNVYLQ 76
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALEALNGTE--LGGRPLKVS 72

RRM_1

pfam00076

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

280-346

1.13e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 46.07 E-value: 1.13e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 280 LLVSNLNTDkIDEDKLFNLFSMYGNIVRIKIL----KNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLE 346
Cdd:pfam00076   1 LFVGNLPPD-TTEEDLKDLFSKFGPIKSIRLVrdetGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM

RNA recognition motif;

390-457

1.62e-06

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 45.66 E-value: 1.62e-06

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002231664  390 IHISALPQDITEDTIHSLVGEHGTIANSRLF--ETNGKT--QALVLFESVEEATEALVEKHASKLDRTNIRI 457
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVrdKETGKSkgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RRM4_PTBP1

cd12701

RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...

390-461

1.85e-06

RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM4 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

Pssm-ID: 410101 [Multi-domain] Cd Length: 76 Bit Score: 45.42 E-value: 1.85e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002231664 390 IHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATEALVEKHASKL-DRTNIRISFSQ 461
Cdd:cd12701     2 LHLSNIPPSVSEEDLKMLFSSNGGMVKGFKFFQKDRKMALIQMGSVEEAIQALIDLHNHDLgENHHLRVSFSK 74

RRM2_PTBP1_like

cd12693

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

293-365

2.50e-06

Pssm-ID: 410093 [Multi-domain] Cd Length: 96 Bit Score: 45.80 E-value: 2.50e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 293 DKLFNLFSMYGNIVRIKIL-KNKPDHALIQMADGLQAELAVLYLKGAMLFGK--KLEVNYSKYPTVTA---DPDARDYS 365
Cdd:cd12693    18 DVLHQIFSKFGTVLKIITFtKNNQFQALIQFADAVSAQAAKLSLDGQNIYNGccTLRIDFSKLTSLNVkynNDKSRDYT 96

RRM4_PTBP2

cd12702

RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 2 ...

386-461

2.50e-06

RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM4 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 241146 [Multi-domain] Cd Length: 80 Bit Score: 45.39 E-value: 2.50e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002231664 386 PTKMIHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKtQALVLFESVEEATEALVEKHASKL-DRTNIRISFSQ 461
Cdd:cd12702     2 PSATLHLSNIPPSVAEEDLRTLFANTGGTVKAFKFFQDHK-MALLQMSTVEEAIQALIDLHNYNLgENHHLRVSFSK 77

RRM_ALKBH8

cd12431

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...

114-168

2.74e-06

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.

Pssm-ID: 409865 [Multi-domain] Cd Length: 80 Bit Score: 45.26 E-value: 2.74e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 114 ITIEVLHQVFSPYGFVEKIVTF-QKSAGFqtlIQYQSRQSAIQAYGALHGRNIYDG 168
Cdd:cd12431    15 VSREQLLEVFEKYGTVEDIVMLpGKPYSF---VSFKSVEEAAKAYNALNGKELELP 67

RRM2_PTBP1_hnRNPL_like

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

10-87

3.17e-06

Pssm-ID: 409856 [Multi-domain] Cd Length: 85 Bit Score: 45.26 E-value: 3.17e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664  10 IRNVGHEISESELLQVVQPFGTVAKLVMLRaKN---QALVQMEDLASAVNVIQYYNtiqpsvrGRNVY-------LQYSS 79
Cdd:cd12422     6 VTNLLYPVTVDVLHQVFSPYGAVEKIVIFE-KGtgvQALVQFDSVESAEAAKKALN-------GRNIYdgcctldIQFSR 77


                  ....*...
gi 1002231664  80 HQELTTDQ 87
Cdd:cd12422    78 LKELTVKY 85

RRM2_MEI2_EAR1_like

cd12276

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...

279-347

6.55e-06

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.

Pssm-ID: 409718 [Multi-domain] Cd Length: 71 Bit Score: 43.78 E-value: 6.55e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 279 TLLVSNLNTDkIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEV 347
Cdd:cd12276     3 TLLVFNLDAP-VSNDELKSLFSKFGEIKEIRPTPDKPSQKFVEFYDVRDAEAALDGLNGRELLGGKLKV 70

RRM_Nab3p

cd12342

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...

280-351

6.85e-06

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.

Pssm-ID: 240788 [Multi-domain] Cd Length: 71 Bit Score: 43.59 E-value: 6.85e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002231664 280 LLVSNLNTDKIDEDKLFNLFSMYGNIVRIKIlknKPDHALIQM------ADGLQAElavlylKGAMLFGKKLEVNYSK 351
Cdd:cd12342     2 LFIGNLPTKRVSKEDLFRIFSPYGHLMQIVI---KNAFGFVQFdspqscRNAIECE------QGEMNRGKKLHLEVSK 70

RRM1_PTBP1_hnRNPL_like

cd12421

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

390-440

1.18e-05

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.

Pssm-ID: 409855 [Multi-domain] Cd Length: 74 Bit Score: 43.33 E-value: 1.18e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 390 IHISALPQDITEDTIHSLVGEHGTIANSRLfeTNGKTQALVLFESVEEATE 440
Cdd:cd12421     2 VHIRNLPPDATEADLVALGLPFGKVTNVLL--LKGKNQALVEMEDVESASS 50

RRM_1

pfam00076

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

390-456

1.35e-05

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 42.99 E-value: 1.35e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 390 IHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKT---QALVLFESVEEATEALVEKHASKLDRTNIR 456
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM2_PTBP1_hnRNPL_like

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

280-351

1.69e-05

Pssm-ID: 409856 [Multi-domain] Cd Length: 85 Bit Score: 42.95 E-value: 1.69e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 280 LLVSNLNTD-KIDEDKLFNLFSMYGNIVRIKIL-KNKPDHALIQMADGLQAELAVLYLKGAMLFGK--KLEVNYSK 351
Cdd:cd12422     2 LLVTVTNLLyPVTVDVLHQVFSPYGAVEKIVIFeKGTGVQALVQFDSVESAEAAKKALNGRNIYDGccTLDIQFSR 77

RRM4_PTBPH3

cd12426

RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 ...

4-54

1.99e-05

Pssm-ID: 409860 [Multi-domain] Cd Length: 79 Bit Score: 42.58 E-value: 1.99e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1002231664   4 PSKVIHIRNVGHEISESELLQVVQPFGTV--AKLVMLRAKNQALVQMEDLASA 54
Cdd:cd12426     6 PTKMIHVSSLPQDVTEEDVLNHLQEHGAIvnTKVFESNGKKQALVLFENEEQA 58

RRM_SF

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

112-167

2.01e-05

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 42.27 E-value: 2.01e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 112 YPITIEVLHQVFSPYGFVEKIVTFQKSAGFQT---LIQYQSRQSAIQAYGALHGRNIYD 167
Cdd:cd00590     8 PDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKgfaFVEFESPEDAEKALEALNGTELGG 66

RRM1_RIM4_like

cd12453

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...

280-351

3.34e-05

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.

Pssm-ID: 409887 [Multi-domain] Cd Length: 86 Bit Score: 42.40 E-value: 3.34e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002231664 280 LLVSNLNTDKIDED---KLFNLFSMYGNIVRIKILK---NKPdHALIQMADGLQAELAVLYLKGAMLFGKKLEVNYSK 351
Cdd:cd12453     5 LFVASLSSARSDEElcaAVTNHFSKWGELLNVKVLKdwsNRP-YAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKAK 81

ELAV_HUD_SF

TIGR01661

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...

114-349

3.37e-05

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

Pssm-ID: 273741 [Multi-domain] Cd Length: 352 Bit Score: 45.70 E-value: 3.37e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 114 ITIEVLHQVFSPYG-------FVEKIVTFQKSAGFqtlIQYQSRQSAIQAYGALHGrNIYDGCC-QLDIQYSNlselqvh 185
Cdd:TIGR01661 101 MTQHELESIFSPFGqiitsriLSDNVTGLSKGVGF---IRFDKRDEADRAIKTLNG-TTPSGCTePITVKFAN------- 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 186 ynndrsrdftNPSLPTEQRSRSSQPSYNDPS------SLFGFQQPGDPYAQVSMDISYKASAALCYfnISPYQMSKAAMI 259
Cdd:TIGR01661 170 ----------NPSSSNSKGLLSQLEAVQNPQttrvplSTILTAAGIGPMHHAAARFRPSAGDFTAV--LAHQQQQHAVAQ 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002231664 260 AAAFGGTLPPGVSGIND--------------RCTLLVSNLNTDKiDEDKLFNLFSMYGNIVRIKILK----NK-PDHALI 320
Cdd:TIGR01661 238 QHAAQRASPPATDGQTAglaagaqisasdgaGYCIFVYNLSPDT-DETVLWQLFGPFGAVQNVKIIRdlttNQcKGYGFV 316

                         250       260
                  ....*....|....*....|....*....
gi 1002231664 321 QMADGLQAELAVLYLKGAMLFGKKLEVNY 349
Cdd:TIGR01661 317 SMTNYDEAAMAILSLNGYTLGNRVLQVSF 345

RRM_ZCRB1

cd12393

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...

277-347

4.77e-05

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.

Pssm-ID: 409827 [Multi-domain] Cd Length: 76 Bit Score: 41.50 E-value: 4.77e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002231664 277 RCTLLVSNLNTDKIDEDkLFNLFSMYGNIVRIKILKNKPDH-----ALIQMADGLQAELAVLYLKGAMLFGKKLEV 347
Cdd:cd12393     1 KSTVYVSNLPFSLTNND-LHQIFSKYGKVVKVTILKDKETRkskgvAFVLFLDRESAHNAVRAMNNKELFGRTLKC 75

RRM1_2_CID8_like

cd12225

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...

279-353

4.78e-05

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

Pssm-ID: 409672 [Multi-domain] Cd Length: 76 Bit Score: 41.68 E-value: 4.78e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002231664 279 TLLVSNLNTdKIDEDKLFNLFSMYGNIVRIKILKNKPDH--ALIQMADgLQAELAVLYLKGAMLFGKKLEVNYSKYP 353
Cdd:cd12225     2 TIHVGGIDG-SLSEDELADYFSNCGEVTQVRLCGDRVHTrfAWVEFAT-DASALSALNLDGTTLGGHPLRVSPSKTA 76

RRM1_MATR3

cd12714

RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the ...

21-78

5.30e-05

RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the RRM1 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.

Pssm-ID: 410113 [Multi-domain] Cd Length: 76 Bit Score: 41.46 E-value: 5.30e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002231664  21 ELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYS 78
Cdd:cd12714    17 QLLQLAEPFGIITNHLILNKINEAFIEMATTEEAQAAVDYYMTTPALVFGKPVRVHLS 74

RRM1_RBM26_like

cd12257

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...

277-331

5.61e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

Pssm-ID: 409702 [Multi-domain] Cd Length: 72 Bit Score: 41.01 E-value: 5.61e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1002231664 277 RCTLLVSNLNTDKIDEDKLFNLFSMYGNIVRIKILKNkPDHALIQMADGLQAELA 331
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYN-PESALVQFSTSEEANKA 54

RRM2_MEI2_like

cd12529

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...

279-347

6.44e-05

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

Pssm-ID: 409948 [Multi-domain] Cd Length: 71 Bit Score: 40.95 E-value: 6.44e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002231664 279 TLLVSNLNTdKIDEDKLFNLFSMYGNIVRIKILKNKPDHALIQMADGLQAELAVLYLKGAMLFGKKLEV 347
Cdd:cd12529     3 TLVVFNLDP-SISNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70

RRM1_PTBPH1_PTBPH2

cd12686

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 ...

386-456

7.55e-05

Pssm-ID: 410087 [Multi-domain] Cd Length: 81 Bit Score: 40.95 E-value: 7.55e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 386 PTKMIHISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATeALVEKHASKLDRTNIR 456
Cdd:cd12686     1 PSKVLHLRNLPWECTEEELIELCKPFGTVVNTKCNVGANKNQAFVEFADLNQAI-SMVSYYASSSEPAQVR 70

RRM1_2_NP220

cd12716

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...

7-80

9.04e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410115 [Multi-domain] Cd Length: 76 Bit Score: 40.84 E-value: 9.04e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002231664   7 VIHIRNVGHE-ISESELLQVVQPFGTVAKLVMLRAKNQALVQMEDLASAVNVIQYYNTIQPSVRGRNVYLQYSSH 80
Cdd:cd12716     2 VVLISNLPEKgYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76

RRM3_TIA1_like

cd12354

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...

115-165

1.15e-04

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

Pssm-ID: 409790 [Multi-domain] Cd Length: 71 Bit Score: 40.34 E-value: 1.15e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002231664 115 TIEVLHQVFSPYGFVEKIVTFqKSAGFqTLIQYQSRQSAIQAYGALHGRNI 165
Cdd:cd12354    13 TEALLQQTFSPFGQILEVRVF-PDKGY-AFIRFDSHEAATHAIVSVNGTII 61

RRM1_Prp24

cd12296

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...

392-458

1.26e-04

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

Pssm-ID: 409737 [Multi-domain] Cd Length: 71 Bit Score: 40.33 E-value: 1.26e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002231664 392 ISALPQDITEDTIHSLVGEHGTIANSRLFETNGKTQALVLFESVEEATEALVeKHASKLDRTNIRIS 458
Cdd:cd12296     5 VKNLPKSITENKIRQFFKDCGEIREVKILESGNGLVAVIEFETEDEALAALT-KDHKRIGGNEISVS 70

RRM