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Conserved domains on  [gi|225543110|ref|NP_663368|]
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YTH domain-containing family protein 2 [Mus musculus]

Protein Classification

YTH domain-containing protein( domain architecture ID 10514278)

YTH (YT521-B homology) domain-containing protein acts as a N6-methyladenosine (m6A) reader to read m6A marks and transduces their downstream regulatory effects by altering m6A-mRNA metabolism processes

CATH:  3.10.590.10
Gene Ontology:  GO:0061157|GO:0003729|GO:0003730|GO:0043488|GO:1990247
PubMed:  12368078
SCOP:  4004472

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH pfam04146
YT521-B-like domain; A protein of the YTH family has been shown to selectively remove ...
 411-544 1.72e-69

YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily.


:

Pssm-ID: 461195  Cd Length: 135  Bit Score: 220.06  E-value: 1.72e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  411 RVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSmngKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVW--SQ 488
Cdd:pfam04146   2 RFFIIKSLNEENIHLSIKYGIWATQPHNNKRLNEAFKE---SKNVYLIFSVNKSGHFQGYARMTSPVDFDPSFIFWeaDS 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 225543110  489 DKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKII 544
Cdd:pfam04146  79 DKWGGPFKVEWLSVKDLPFSRLRHLRNPLNENKPVKISRDGQEIEPEVGRQLLKLF 134
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 200-359 8.92e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.15  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  200 ASSVPKVVGSAVGSGSITSNIVASSSLPPATIAPPKP-----ASWADIASKPAKQQP--KLKTKNGIAGSSLPPPPIKHN 272
Cdd:PHA03247 2815 AAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSPaaKPAAPARPPVRRLARPAVSRS 2894

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  273 MDIGTWDNKGPVAKAPSQALVQNIGQPTQgSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTRWV 352
Cdd:PHA03247 2895 TESFALPPDQPERPPQPQAPPPPQPQPQP-PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVA 2973


                  ....*..
gi 225543110  353 APRNRGS 359
Cdd:PHA03247 2974 VPRFRVP 2980
 
Name Accession Description Interval E-value
YTH pfam04146
YT521-B-like domain; A protein of the YTH family has been shown to selectively remove ...
 411-544 1.72e-69

YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily.


Pssm-ID: 461195  Cd Length: 135  Bit Score: 220.06  E-value: 1.72e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  411 RVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSmngKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVW--SQ 488
Cdd:pfam04146   2 RFFIIKSLNEENIHLSIKYGIWATQPHNNKRLNEAFKE---SKNVYLIFSVNKSGHFQGYARMTSPVDFDPSFIFWeaDS 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 225543110  489 DKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKII 544
Cdd:pfam04146  79 DKWGGPFKVEWLSVKDLPFSRLRHLRNPLNENKPVKISRDGQEIEPEVGRQLLKLF 134
YTH cd21134
YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily; ...
 411-544 1.56e-67

YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily; Individual members of the YTH family have been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. In general, eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or in other forms of silencing. The YTH domain is a novel RNA-binding domain that has been shown to bind to short, degenerate, single-stranded RNA motifs that loosely follow a consensus sequence. It belongs to the larger PUA superfamily.


Pssm-ID: 410979  Cd Length: 133  Bit Score: 215.12  E-value: 1.56e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110 411 RVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSmngKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCA--GVWSQ 488
Cdd:cd21134    1 RFFIIKSNNEENIHLSIKYGVWATQPHNEKKLNQAFRE---SGNVYLIFSVNGSGHFQGYARMTSPPDPNRSPswPWWSQ 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 225543110 489 DKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKII 544
Cdd:cd21134   78 DKLGGPFKVEWLRVKDLPFSKLRHLKNPLNENKPVTISRDGQEIEPEVGEQLLKLF 133
PHA03247 PHA03247
large tegument protein UL36; Provisional
 200-359 8.92e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.15  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  200 ASSVPKVVGSAVGSGSITSNIVASSSLPPATIAPPKP-----ASWADIASKPAKQQP--KLKTKNGIAGSSLPPPPIKHN 272
Cdd:PHA03247 2815 AAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSPaaKPAAPARPPVRRLARPAVSRS 2894

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  273 MDIGTWDNKGPVAKAPSQALVQNIGQPTQgSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTRWV 352
Cdd:PHA03247 2895 TESFALPPDQPERPPQPQAPPPPQPQPQP-PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVA 2973


                  ....*..
gi 225543110  353 APRNRGS 359
Cdd:PHA03247 2974 VPRFRVP 2980
 
Name Accession Description Interval E-value
YTH pfam04146
YT521-B-like domain; A protein of the YTH family has been shown to selectively remove ...
 411-544 1.72e-69

YT521-B-like domain; A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily.


Pssm-ID: 461195  Cd Length: 135  Bit Score: 220.06  E-value: 1.72e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  411 RVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSmngKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVW--SQ 488
Cdd:pfam04146   2 RFFIIKSLNEENIHLSIKYGIWATQPHNNKRLNEAFKE---SKNVYLIFSVNKSGHFQGYARMTSPVDFDPSFIFWeaDS 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 225543110  489 DKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKII 544
Cdd:pfam04146  79 DKWGGPFKVEWLSVKDLPFSRLRHLRNPLNENKPVKISRDGQEIEPEVGRQLLKLF 134
YTH cd21134
YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily; ...
 411-544 1.56e-67

YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily; Individual members of the YTH family have been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. In general, eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or in other forms of silencing. The YTH domain is a novel RNA-binding domain that has been shown to bind to short, degenerate, single-stranded RNA motifs that loosely follow a consensus sequence. It belongs to the larger PUA superfamily.


Pssm-ID: 410979  Cd Length: 133  Bit Score: 215.12  E-value: 1.56e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110 411 RVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSmngKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCA--GVWSQ 488
Cdd:cd21134    1 RFFIIKSNNEENIHLSIKYGVWATQPHNEKKLNQAFRE---SGNVYLIFSVNGSGHFQGYARMTSPPDPNRSPswPWWSQ 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 225543110 489 DKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKII 544
Cdd:cd21134   78 DKLGGPFKVEWLRVKDLPFSKLRHLKNPLNENKPVTISRDGQEIEPEVGEQLLKLF 133
EVE-like cd21132
EVE and YTH domains belong to the PUA superfamily; The EVE domain was formerly known as DUF55 ...
 411-543 2.06e-16

EVE and YTH domains belong to the PUA superfamily; The EVE domain was formerly known as DUF55 and is thought to be involved in RNA binding. The YTH (YT521-B homology) domain is a novel RNA-binding domain that has been shown to bind to short, degenerate, single-stranded RNA motifs that loosely follow a consensus sequence. Both domains are part of the larger PUA superfamily.


Pssm-ID: 410977  Cd Length: 138  Bit Score: 76.28  E-value: 2.06e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110 411 RVFIIKSYSEDDIHR--SIKYNIWCSTEHGNKRLdaayrsmngKGPVYLLFSVNG--------SGHFCGVAEMKSAVDYN 480
Cdd:cd21132    1 AYWIAIVNEDHVRIGvaGGFKQVWGGKEAPKNRI---------KKGDKLLYYSPKealgdkelLQAFTAIGEVKSEPYYD 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 225543110 481 TCA----GVWSQDKWKGRFDVRWIFVK--DVPNSQLRHIRLENneNKPVTNSRDTQEVPLEKAKQVLKI 543
Cdd:cd21132   72 SKAifspPEMGDGFFPYRRDVEFIKIFedPLSFIELKQDLKFI--WVGHALRRGMFEIPEEDFKLIESL 138
PHA03247 PHA03247
large tegument protein UL36; Provisional
 200-359 8.92e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.15  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  200 ASSVPKVVGSAVGSGSITSNIVASSSLPPATIAPPKP-----ASWADIASKPAKQQP--KLKTKNGIAGSSLPPPPIKHN 272
Cdd:PHA03247 2815 AAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSPaaKPAAPARPPVRRLARPAVSRS 2894

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225543110  273 MDIGTWDNKGPVAKAPSQALVQNIGQPTQgSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTRWV 352
Cdd:PHA03247 2895 TESFALPPDQPERPPQPQAPPPPQPQPQP-PPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVA 2973


                  ....*..
gi 225543110  353 APRNRGS 359
Cdd:PHA03247 2974 VPRFRVP 2980
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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