probable small nuclear ribonucleoprotein F [Oryza sativa Japonica Group]
Protein Classification
small nuclear ribonucleoprotein F( domain architecture ID 10109570)
small nuclear ribonucleoprotein F belongs to the pre-mRNA-binding protein family and is involved in the alternative splicing of various genes
List of domain hits
| Name | Accession | Description | Interval | E-value | ||
| Sm_F | cd01722 | Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
7-75 | 2.63e-49 | ||
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. : Pssm-ID: 212469 Cd Length: 69 Bit Score: 149.67 E-value: 2.63e-49
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| Name | Accession | Description | Interval | E-value | ||
| Sm_F | cd01722 | Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
7-75 | 2.63e-49 | ||
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Pssm-ID: 212469 Cd Length: 69 Bit Score: 149.67 E-value: 2.63e-49
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| LSM | pfam01423 | LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ... |
10-73 | 3.00e-23 | ||
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Pssm-ID: 426258 Cd Length: 66 Bit Score: 83.71 E-value: 3.00e-23
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| Sm | smart00651 | snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ... |
10-74 | 1.75e-21 | ||
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing Pssm-ID: 197820 [Multi-domain] Cd Length: 67 Bit Score: 79.46 E-value: 1.75e-21
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| LSM1 | COG1958 | Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]; |
12-72 | 4.08e-20 | ||
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]; Pssm-ID: 441561 Cd Length: 71 Bit Score: 75.99 E-value: 4.08e-20
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| PRK00737 | PRK00737 | small nuclear ribonucleoprotein; Provisional |
12-73 | 5.84e-16 | ||
small nuclear ribonucleoprotein; Provisional Pssm-ID: 179104 Cd Length: 72 Bit Score: 65.41 E-value: 5.84e-16
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| Name | Accession | Description | Interval | E-value | ||
| Sm_F | cd01722 | Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
7-75 | 2.63e-49 | ||
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Pssm-ID: 212469 Cd Length: 69 Bit Score: 149.67 E-value: 2.63e-49
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| LSm6 | cd01726 | Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ... |
7-72 | 6.52e-25 | ||
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212473 Cd Length: 68 Bit Score: 87.96 E-value: 6.52e-25
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| LSM | pfam01423 | LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ... |
10-73 | 3.00e-23 | ||
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Pssm-ID: 426258 Cd Length: 66 Bit Score: 83.71 E-value: 3.00e-23
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| Sm | smart00651 | snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ... |
10-74 | 1.75e-21 | ||
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing Pssm-ID: 197820 [Multi-domain] Cd Length: 67 Bit Score: 79.46 E-value: 1.75e-21
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| LSM1 | COG1958 | Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]; |
12-72 | 4.08e-20 | ||
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]; Pssm-ID: 441561 Cd Length: 71 Bit Score: 75.99 E-value: 4.08e-20
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| PRK00737 | PRK00737 | small nuclear ribonucleoprotein; Provisional |
12-73 | 5.84e-16 | ||
small nuclear ribonucleoprotein; Provisional Pssm-ID: 179104 Cd Length: 72 Bit Score: 65.41 E-value: 5.84e-16
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| Sm_like | cd00600 | Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ... |
12-74 | 9.55e-14 | ||
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Pssm-ID: 212462 [Multi-domain] Cd Length: 63 Bit Score: 59.57 E-value: 9.55e-14
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| archaeal_Sm1 | cd01731 | archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ... |
12-72 | 2.03e-13 | ||
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Pssm-ID: 212478 Cd Length: 69 Bit Score: 59.13 E-value: 2.03e-13
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| LSm4 | cd01723 | Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ... |
12-79 | 6.07e-10 | ||
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212470 [Multi-domain] Cd Length: 76 Bit Score: 50.27 E-value: 6.07e-10
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| archaeal_LSm | cd11678 | archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ... |
8-71 | 2.29e-08 | ||
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Pssm-ID: 212489 Cd Length: 69 Bit Score: 46.35 E-value: 2.29e-08
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| Sm_D1 | cd01724 | Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
11-72 | 1.60e-06 | ||
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Pssm-ID: 212471 Cd Length: 92 Bit Score: 41.83 E-value: 1.60e-06
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| LSm2 | cd01725 | Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ... |
11-49 | 5.50e-05 | ||
Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212472 Cd Length: 89 Bit Score: 37.95 E-value: 5.50e-05
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| LSm10 | cd01733 | Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form ... |
11-72 | 1.35e-04 | ||
Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Pssm-ID: 212480 Cd Length: 78 Bit Score: 36.75 E-value: 1.35e-04
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| archaeal_Sm_like | cd11679 | archaeal Sm-related protein; Archaeal Sm-related proteins: The Sm proteins are conserved in ... |
12-49 | 1.95e-04 | ||
archaeal Sm-related protein; Archaeal Sm-related proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain. Pssm-ID: 212490 Cd Length: 65 Bit Score: 36.09 E-value: 1.95e-04
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| LSm1 | cd01728 | Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ... |
17-73 | 9.32e-04 | ||
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212475 Cd Length: 74 Bit Score: 34.41 E-value: 9.32e-04
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| Sm_D3 | cd01721 | Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
20-73 | 1.14e-03 | ||
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Pssm-ID: 212468 Cd Length: 70 Bit Score: 34.03 E-value: 1.14e-03
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| LSMD1 | cd06168 | LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ... |
11-51 | 2.59e-03 | ||
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Pssm-ID: 212486 Cd Length: 73 Bit Score: 33.30 E-value: 2.59e-03
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| Sm_G | cd01719 | Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ... |
8-73 | 4.35e-03 | ||
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Pssm-ID: 212466 Cd Length: 70 Bit Score: 32.49 E-value: 4.35e-03
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| LSm3 | cd01730 | Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ... |
20-75 | 8.79e-03 | ||
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212477 Cd Length: 82 Bit Score: 32.20 E-value: 8.79e-03
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| LSm7 | cd01729 | Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ... |
12-52 | 9.11e-03 | ||
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Pssm-ID: 212476 Cd Length: 89 Bit Score: 32.17 E-value: 9.11e-03
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| Blast search parameters | ||||
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