Reviewed,
UniProtKB/Swiss-Prot Q15427 (SF3B4_HUMAN)
Last modified
November 24, 2009.
Version 103.
History...
Clusters with 100%,
90%,
50% identity |
Documents (4) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Splicing factor 3B subunit 4 Alternative name(s): Spliceosome-associated protein 49 Short name=SAP 49 SF3b50 Pre-mRNA-splicing factor SF3b 49 kDa subunit | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) [Complete proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 424 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is further processed into a mature form. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron. |
| Subunit structure | Component of splicing factor SF3B which is composed of at least eight subunits; SF3B1/SAP155/SF3B155, SF3B2/SAP145/SF3B145, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B14A, PHF5A/SF3B14B, SF3B10 and SF3B125. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). SF3B4 interacts directly with SF3B2. |
| Subcellular location | Nucleus By similarity. |
| Sequence similarities | Belongs to the SF3B4 family. Contains 2 RRM (RNA recognition motif) domains. |
Ontologies
| Keywords | |
|---|---|
| Biological process | mRNA processing mRNA splicing |
| Cellular component | Nucleus Spliceosome |
| Domain | Repeat |
| Ligand | RNA-binding |
| PTM | Acetylation Phosphoprotein |
| Technical term | 3D-structure Complete proteome Direct protein sequencing |
| Gene Ontology (GO) | |
| Uncategorized | ? Ref.1 Traceable author statement. Source: ProtInc |
| Biological process | nuclear mRNA splicing, via spliceosome Inferred by curator. Source: HGNC |
| Cellular component | spliceosomal complex Ref.1 Inferred from direct assay. Source: HGNC |
| Molecular function | RNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide bindingInferred from electronic annotation. Source: InterPro protein bindingInferred from physical interaction. Source: IntAct |
| Complete GO annotation... | |
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| ABL1 | P00519 | 1 | EBI-348469,EBI-375543 | |
| FYN | P06241 | 1 | EBI-348469,EBI-515315 | |
| GRB2 | P62993 | 1 | EBI-348469,EBI-401755 | |
| NCK1 | P16333 | 1 | EBI-348469,EBI-389883 | |
| SMNDC1 | O75940 | 1 | EBI-348469,EBI-1052641 | |
| STK19 | P49842 | 1 | EBI-348469,EBI-347581 |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Initiator methionine | 1 | 1 | Removed Ref.5 | ||||||||||||||||||||||||||||||||||||
| Chain | 2 – 424 | 423 | Splicing factor 3B subunit 4 | PRO_0000081955 | |||||||||||||||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||||||||||||||
| Domain | 13 – 91 | 79 | RRM 1 | ||||||||||||||||||||||||||||||||||||
| Domain | 100 – 179 | 80 | RRM 2 | ||||||||||||||||||||||||||||||||||||
| Compositional bias | 215 – 218 | 4 | Poly-Pro | ||||||||||||||||||||||||||||||||||||
| Compositional bias | 262 – 268 | 7 | Poly-Pro | ||||||||||||||||||||||||||||||||||||
Amino acid modifications | |||||||||||||||||||||||||||||||||||||||
| Modified residue | 2 | 1 | N-acetylalanine Ref.5 | ||||||||||||||||||||||||||||||||||||
| Modified residue | 16 | 1 | Phosphotyrosine Ref.10 | ||||||||||||||||||||||||||||||||||||
| Modified residue | 56 | 1 | Phosphotyrosine Ref.9 | ||||||||||||||||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||||||||||||
| Turn | 11 – 13 | 3 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 14 – 18 | 5 | |||||||||||||||||||||||||||||||||||||
| Helix | 26 – 34 | 9 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 39 – 43 | 5 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 48 – 50 | 3 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 57 – 63 | 7 | |||||||||||||||||||||||||||||||||||||
| Helix | 64 – 73 | 10 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 74 – 76 | 3 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 85 – 88 | 4 | |||||||||||||||||||||||||||||||||||||
| Turn | 89 – 92 | 4 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 102 – 105 | 4 | |||||||||||||||||||||||||||||||||||||
| Helix | 113 – 121 | 9 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 126 – 128 | 3 | |||||||||||||||||||||||||||||||||||||
| Turn | 136 – 138 | 3 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 143 – 151 | 9 | |||||||||||||||||||||||||||||||||||||
| Helix | 152 – 160 | 9 | |||||||||||||||||||||||||||||||||||||
| Turn | 161 – 164 | 4 | |||||||||||||||||||||||||||||||||||||
| Beta strand | 173 – 177 | 5 | |||||||||||||||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "The prespliceosome components SAP 49 and SAP 145 interact in a complex implicated in tethering U2 snRNP to the branch site." Champion-Arnaud P., Reed R. Genes Dev. 8:1974-1983(1994) [PubMed: 7958871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
| [2] | "The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. Bentley D.R.Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [3] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin and Testis. |
| [5] | Bienvenut W.V., Lilla S., von Kriegsheim A., Lempens A., Kolch W. Submitted (DEC-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-23, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY. Tissue: Ovarian carcinoma. |
| [6] | "Functional association of U2 snRNP with the ATP-independent spliceosomal complex E." Das R., Zhou Z., Reed R. Mol. Cell 5:779-787(2000) [PubMed: 10882114] [Abstract] Cited for: CHARACTERIZATION OF THE SPLICEOSOME. |
| [7] | "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein." Will C.L., Urlaub H., Achsel T., Gentzel M., Wilm M., Luehrmann R. EMBO J. 21:4978-4988(2002) [PubMed: 12234937] [Abstract] Cited for: IDENTIFICATION IN THE SF3B COMPLEX. |
| [8] | "Molecular architecture of the multiprotein splicing factor SF3b." Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H. Science 300:980-984(2003) [PubMed: 12738865] [Abstract] Cited for: IDENTIFICATION IN THE SF3B COMPLEX, ELECTRON MICROSCOPY OF THE SF3B COMPLEX. |
| [9] | "Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-56, MASS SPECTROMETRY. |
| [10] | "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer." Rikova K., Guo A., Zeng Q., Possemato A., Yu J., Haack H., Nardone J., Lee K., Reeves C., Li Y., Hu Y., Tan Z., Stokes M., Sullivan L., Mitchell J., Wetzel R., Macneill J., Ren J.M. Comb M.J.Cell 131:1190-1203(2007) [PubMed: 18083107] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-16, MASS SPECTROMETRY. |
| [11] | Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. |
| [12] | "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY. |
| [13] | "Solution structure of RRM domains in splicing factor 3B." RIKEN structural genomics initiative (RSGI) Submitted (NOV-2005) to the PDB data bank Cited for: STRUCTURE BY NMR OF 4-184. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| L35013 Genomic DNA. Translation: AAA60300.1. AL591493, AL590487 Genomic DNA. Translation: CAI12554.1. AL590487, AL591493 Genomic DNA. Translation: CAI12648.1. CH471121 Genomic DNA. Translation: EAW53595.1. BC004273 mRNA. Translation: AAH04273.1. BC013886 mRNA. Translation: AAH13886.1. BC090883 mRNA. Translation: AAH90883.1. | |||||||||||||||||||
| IPI | IPI00017339. | ||||||||||||||||||
| PIR | A54964. | ||||||||||||||||||
| RefSeq | NP_005841.1. | ||||||||||||||||||
| UniGene | Hs.516160 | ||||||||||||||||||
3D structure databases | |||||||||||||||||||
| |||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||
| IntAct | Q15427. 11 interactions. | ||||||||||||||||||
| STRING | Q15427. | ||||||||||||||||||
PTM databases | |||||||||||||||||||
| PhosphoSite | Q15427. | ||||||||||||||||||
Proteomic databases | |||||||||||||||||||
| PeptideAtlas | Q15427. | ||||||||||||||||||
| PRIDE | Q15427. | ||||||||||||||||||
Genome annotation databases | |||||||||||||||||||
| Ensembl | ENST00000271628; ENSP00000271628; ENSG00000143368; Homo sapiens. [Genome view] | ||||||||||||||||||
| GeneID | 10262. | ||||||||||||||||||
| KEGG | hsa:10262. | ||||||||||||||||||
| UCSC | uc001etj.1. human. | ||||||||||||||||||
Organism-specific databases | |||||||||||||||||||
| CTD | 10262. | ||||||||||||||||||
| GeneCards | GC01M148161. | ||||||||||||||||||
| H-InvDB | HIX0001007. | ||||||||||||||||||
| HGNC | HGNC:10771. SF3B4. | ||||||||||||||||||
| MIM | 605593. gene. | ||||||||||||||||||
| PharmGKB | PA35689. | ||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||
| HOGENOM | Q15427. | ||||||||||||||||||
| HOVERGEN | Q15427. | ||||||||||||||||||
| OMA | MGMPPRA | ||||||||||||||||||
| OrthoDB | EOG998XKQ | ||||||||||||||||||
Enzyme and pathway databases | |||||||||||||||||||
| Reactome | REACT_125. Processing of Capped Intron-Containing Pre-mRNA. REACT_71. Gene Expression. | ||||||||||||||||||
Gene expression databases | |||||||||||||||||||
| ArrayExpress | Q15427. | ||||||||||||||||||
| Bgee | Q15427. | ||||||||||||||||||
| CleanEx | HS_SF3B4. | ||||||||||||||||||
| Genevestigator | Q15427. | ||||||||||||||||||
| GermOnline | ENSG00000143368. Homo sapiens. | ||||||||||||||||||
Family and domain databases | |||||||||||||||||||
| InterPro | IPR012677. a_b_plait_nuc_bd. IPR000504. RRM_RNP1. [Graphical view] | ||||||||||||||||||
| Gene3D | G3DSA:3.30.70.330. a_b_plait_nuc_bd. 2 hits. | ||||||||||||||||||
| Pfam | PF00076. RRM_1. 2 hits. [Graphical view] | ||||||||||||||||||
| SMART | SM00360. RRM. 2 hits. [Graphical view] | ||||||||||||||||||
| PROSITE | PS50102. RRM. 2 hits. [Graphical view] | ||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||
Other Resources | |||||||||||||||||||
| NextBio | 38880. | ||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||
Entry information
| Entry name | SF3B4_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q15427 Secondary accession number(s): Q5SZ63 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 1 Human chromosome 1: entries, gene names and cross-references to MIM |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with


