UniProtKB - Q15427 (SF3B4_HUMAN)
Splicing factor 3B subunit 4
SF3B4
Functioni
Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643).
SF3B complex is 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 (PubMed:12234937).
May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well (PubMed:10882114).
Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077).
4 PublicationsGO - Molecular functioni
- RNA binding Source: UniProtKB
- splicing factor binding Source: UniProtKB
GO - Biological processi
- mRNA processing Source: ProtInc
- mRNA splicing, via spliceosome Source: UniProtKB
- positive regulation of mRNA splicing, via spliceosome Source: GO_Central
- RNA splicing Source: ProtInc
- RNA splicing, via transesterification reactions Source: ProtInc
Keywordsi
Molecular function | RNA-binding |
Biological process | mRNA processing, mRNA splicing |
Enzyme and pathway databases
PathwayCommonsi | Q15427 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
SignaLinki | Q15427 |
Names & Taxonomyi
Protein namesi | Recommended name: Splicing factor 3B subunit 4Alternative name(s): Pre-mRNA-splicing factor SF3b 49 kDa subunit Spliceosome-associated protein 49 Short name: SAP 49 |
Gene namesi | Name:SF3B4 Synonyms:SAP49 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:10771, SF3B4 |
MIMi | 605593, gene |
neXtProti | NX_Q15427 |
VEuPathDBi | HostDB:ENSG00000143368 |
Subcellular locationi
Nucleus
- Nucleus 2 Publications
Nucleus
- nucleoplasm Source: Reactome
- nucleus Source: UniProtKB
- spliceosomal complex Source: HGNC-UCL
- U12-type spliceosomal complex Source: UniProtKB
- U2-type precatalytic spliceosome Source: UniProtKB
- U2-type spliceosomal complex Source: ComplexPortal
Keywords - Cellular componenti
Nucleus, SpliceosomePathology & Biotechi
Involvement in diseasei
Acrofacial dysostosis 1, Nager type (AFD1)1 Publication
Organism-specific databases
DisGeNETi | 10262 |
MalaCardsi | SF3B4 |
MIMi | 154400, phenotype |
OpenTargetsi | ENSG00000143368 |
Orphaneti | 1788, Acrofacial dysostosis, Rodriguez type 245, Nager syndrome |
PharmGKBi | PA35689 |
Miscellaneous databases
Pharosi | Q15427, Tbio |
Genetic variation databases
BioMutai | SF3B4 |
DMDMi | 2500587 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources1 Publication | |||
ChainiPRO_0000081955 | 2 – 424 | Splicing factor 3B subunit 4Add BLAST | 423 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylalanineCombined sources1 Publication | 1 | |
Modified residuei | 56 | PhosphotyrosineCombined sources | 1 |
Keywords - PTMi
Acetylation, PhosphoproteinProteomic databases
EPDi | Q15427 |
jPOSTi | Q15427 |
MassIVEi | Q15427 |
MaxQBi | Q15427 |
PaxDbi | Q15427 |
PeptideAtlasi | Q15427 |
PRIDEi | Q15427 |
ProteomicsDBi | 60587 |
PTM databases
GlyGeni | Q15427, 1 site, 1 O-linked glycan (1 site) |
iPTMneti | Q15427 |
PhosphoSitePlusi | Q15427 |
SwissPalmi | Q15427 |
Expressioni
Gene expression databases
Bgeei | ENSG00000143368, Expressed in mucosa of transverse colon and 217 other tissues |
ExpressionAtlasi | Q15427, baseline and differential |
Genevisiblei | Q15427, HS |
Organism-specific databases
HPAi | ENSG00000143368, Low tissue specificity |
Interactioni
Subunit structurei
Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42 (PubMed:12234937, PubMed:12738865, PubMed:27720643, PubMed:28541300). SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP) (PubMed:12234937).
Interacts directly with SF3B2.
Found in a complex with PRMT9, SF3B2 and SF3B4 (PubMed:25737013). The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2 (PubMed:27720643).
Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077).
6 PublicationsBinary interactionsi
Q15427
GO - Molecular functioni
- splicing factor binding Source: UniProtKB
Protein-protein interaction databases
BioGRIDi | 115554, 337 interactors |
ComplexPortali | CPX-2227, SF3B complex |
CORUMi | Q15427 |
IntActi | Q15427, 88 interactors |
MINTi | Q15427 |
STRINGi | 9606.ENSP00000271628 |
Miscellaneous databases
RNActi | Q15427, protein |
Structurei
Secondary structure
3D structure databases
AlphaFoldDBi | Q15427 |
SMRi | Q15427 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q15427 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 13 – 91 | RRM 1PROSITE-ProRule annotationAdd BLAST | 79 | |
Domaini | 100 – 179 | RRM 2PROSITE-ProRule annotationAdd BLAST | 80 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 207 – 424 | DisorderedSequence analysisAdd BLAST | 218 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 232 – 274 | Pro residuesSequence analysisAdd BLAST | 43 | |
Compositional biasi | 327 – 424 | Pro residuesSequence analysisAdd BLAST | 98 |
Sequence similaritiesi
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | KOG0131, Eukaryota |
GeneTreei | ENSGT00870000136537 |
HOGENOMi | CLU_012062_21_0_1 |
InParanoidi | Q15427 |
OMAi | HWEQNKE |
OrthoDBi | 1479417at2759 |
PhylomeDBi | Q15427 |
TreeFami | TF300890 |
Family and domain databases
CDDi | cd12334, RRM1_SF3B4, 1 hit cd12335, RRM2_SF3B4, 1 hit |
Gene3Di | 3.30.70.330, 2 hits |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom IPR034158, SF3B4_RRM1 IPR034159, SF3B4_RRM2 |
Pfami | View protein in Pfam PF00076, RRM_1, 2 hits |
SMARTi | View protein in SMART SM00360, RRM, 2 hits |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 2 hits |
(1+)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All
10 20 30 40 50
MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT
60 70 80 90 100
GQHQGYGFVE FLSEEDADYA IKIMNMIKLY GKPIRVNKAS AHNKNLDVGA
110 120 130 140 150
NIFIGNLDPE IDEKLLYDTF SAFGVILQTP KIMRDPDTGN SKGYAFINFA
160 170 180 190 200
SFDASDAAIE AMNGQYLCNR PITVSYAFKK DSKGERHGSA AERLLAAQNP
210 220 230 240 250
LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP GSFPPPVPPP
260 270 280 290 300
GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG
310 320 330 340 350
MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG
360 370 380 390 400
MPPRGPPFGS PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP
410 420
LPPPRPTPRP PVPPRGPLRG PLPQ
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketQ5SZ64 | Q5SZ64_HUMAN | Splicing factor 3B subunit 4 | SF3B4 RP11-196G18.20-002 | 190 | Annotation score: |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | 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 |
CCDSi | CCDS72900.1 |
PIRi | A54964 |
RefSeqi | NP_005841.1, NM_005850.4 |
Genome annotation databases
Ensembli | ENST00000271628.9; ENSP00000271628.8; ENSG00000143368.10 |
GeneIDi | 10262 |
KEGGi | hsa:10262 |
MANE-Selecti | ENST00000271628.9; ENSP00000271628.8; NM_005850.5; NP_005841.1 |
UCSCi | uc001etk.3, human |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | 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 |
CCDSi | CCDS72900.1 |
PIRi | A54964 |
RefSeqi | NP_005841.1, NM_005850.4 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1X5T | NMR | - | A | 102-184 | [»] | |
5GVQ | NMR | - | A | 5-96 | [»] | |
5Z56 | electron microscopy | 5.10 | 4 | 1-424 | [»] | |
5Z57 | electron microscopy | 6.50 | 4 | 1-424 | [»] | |
5Z58 | electron microscopy | 4.90 | 4 | 1-424 | [»] | |
6AH0 | electron microscopy | 5.70 | 4 | 1-424 | [»] | |
6AHD | electron microscopy | 3.80 | 4 | 1-424 | [»] | |
6QX9 | electron microscopy | 3.28 | B4 | 1-424 | [»] | |
6Y53 | electron microscopy | 7.10 | o | 1-424 | [»] | |
6Y5Q | electron microscopy | 7.10 | o | 1-424 | [»] | |
7ABG | electron microscopy | 7.80 | w | 1-424 | [»] | |
7ABH | electron microscopy | 4.50 | w | 1-424 | [»] | |
7ABI | electron microscopy | 8.00 | w | 1-424 | [»] | |
7DVQ | electron microscopy | 2.89 | 4 | 1-424 | [»] | |
7ONB | electron microscopy | 3.10 | K | 1-424 | [»] | |
AlphaFoldDBi | Q15427 | |||||
SMRi | Q15427 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 115554, 337 interactors |
ComplexPortali | CPX-2227, SF3B complex |
CORUMi | Q15427 |
IntActi | Q15427, 88 interactors |
MINTi | Q15427 |
STRINGi | 9606.ENSP00000271628 |
PTM databases
GlyGeni | Q15427, 1 site, 1 O-linked glycan (1 site) |
iPTMneti | Q15427 |
PhosphoSitePlusi | Q15427 |
SwissPalmi | Q15427 |
Genetic variation databases
BioMutai | SF3B4 |
DMDMi | 2500587 |
Proteomic databases
EPDi | Q15427 |
jPOSTi | Q15427 |
MassIVEi | Q15427 |
MaxQBi | Q15427 |
PaxDbi | Q15427 |
PeptideAtlasi | Q15427 |
PRIDEi | Q15427 |
ProteomicsDBi | 60587 |
Protocols and materials databases
Antibodypediai | 20268, 332 antibodies from 37 providers |
DNASUi | 10262 |
Genome annotation databases
Ensembli | ENST00000271628.9; ENSP00000271628.8; ENSG00000143368.10 |
GeneIDi | 10262 |
KEGGi | hsa:10262 |
MANE-Selecti | ENST00000271628.9; ENSP00000271628.8; NM_005850.5; NP_005841.1 |
UCSCi | uc001etk.3, human |
Organism-specific databases
CTDi | 10262 |
DisGeNETi | 10262 |
GeneCardsi | SF3B4 |
HGNCi | HGNC:10771, SF3B4 |
HPAi | ENSG00000143368, Low tissue specificity |
MalaCardsi | SF3B4 |
MIMi | 154400, phenotype 605593, gene |
neXtProti | NX_Q15427 |
OpenTargetsi | ENSG00000143368 |
Orphaneti | 1788, Acrofacial dysostosis, Rodriguez type 245, Nager syndrome |
PharmGKBi | PA35689 |
VEuPathDBi | HostDB:ENSG00000143368 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG0131, Eukaryota |
GeneTreei | ENSGT00870000136537 |
HOGENOMi | CLU_012062_21_0_1 |
InParanoidi | Q15427 |
OMAi | HWEQNKE |
OrthoDBi | 1479417at2759 |
PhylomeDBi | Q15427 |
TreeFami | TF300890 |
Enzyme and pathway databases
PathwayCommonsi | Q15427 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
SignaLinki | Q15427 |
Miscellaneous databases
BioGRID-ORCSi | 10262, 781 hits in 1081 CRISPR screens |
ChiTaRSi | SF3B4, human |
EvolutionaryTracei | Q15427 |
GeneWikii | SF3B4 |
GenomeRNAii | 10262 |
Pharosi | Q15427, Tbio |
PROi | PR:Q15427 |
RNActi | Q15427, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000143368, Expressed in mucosa of transverse colon and 217 other tissues |
ExpressionAtlasi | Q15427, baseline and differential |
Genevisiblei | Q15427, HS |
Family and domain databases
CDDi | cd12334, RRM1_SF3B4, 1 hit cd12335, RRM2_SF3B4, 1 hit |
Gene3Di | 3.30.70.330, 2 hits |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom IPR034158, SF3B4_RRM1 IPR034159, SF3B4_RRM2 |
Pfami | View protein in Pfam PF00076, RRM_1, 2 hits |
SMARTi | View protein in SMART SM00360, RRM, 2 hits |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 2 hits |
MobiDBi | Search... |
Entry informationi
Entry namei | SF3B4_HUMAN | |
Accessioni | Q15427Primary (citable) accession number: Q15427 Secondary accession number(s): Q5SZ63 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | November 1, 1997 |
Last sequence update: | November 1, 1996 | |
Last modified: | May 25, 2022 | |
This is version 215 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
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. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- 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