UniProtKB - Q9Y3B4 (SF3B6_HUMAN)
Protein
Splicing factor 3B subunit 6
Gene
SF3B6
Organism
Homo sapiens (Human)
Status
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 (PubMed:12234937). Directly contacts the pre-mRNA branch site adenosine for the first catalytic step of splicing (PubMed:16432215). Enters the spliceosome and associates with the pre-mRNA branch site as part of the 17S U2 or, in the case of the minor spliceosome, as part of the 18S U11/U12 snRNP complex, and thus may facilitate the interaction of these snRNP with the branch sites of U2 and U12 respectively (PubMed:16432215).3 Publications
GO - Molecular functioni
- mRNA binding Source: UniProtKB
- RNA binding Source: UniProtKB
GO - Biological processi
- blastocyst formation Source: Ensembl
- mRNA splicing, via spliceosome Source: UniProtKB
Keywordsi
Molecular function | RNA-binding |
Biological process | mRNA processing, mRNA splicing |
Enzyme and pathway databases
PathwayCommonsi | Q9Y3B4 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
Names & Taxonomyi
Protein namesi | Recommended name: Splicing factor 3B subunit 6Alternative name(s): Pre-mRNA branch site protein p14 SF3b 14 kDa subunit Short name: SF3B14a Spliceosome-associated protein, 14-kDa Splicing factor 3b, subunit 6, 14kDa |
Gene namesi | Name:SF3B6 Synonyms:SAP14, SF3B14, SF3B14A ORF Names:CGI-110, HSPC175, HT006 |
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
EuPathDBi | HostDB:ENSG00000115128.6 |
HGNCi | HGNC:30096, SF3B6 |
MIMi | 607835, gene |
neXtProti | NX_Q9Y3B4 |
Subcellular locationi
Nucleus
- Nucleus 2 Publications
Nucleus
- catalytic step 2 spliceosome Source: GO_Central
- nucleoplasm Source: Reactome
- nucleus Source: UniProtKB
- precatalytic spliceosome Source: GO_Central
- U12-type spliceosomal complex Source: UniProtKB
- U2 snRNP Source: GO_Central
- U2-type spliceosomal complex Source: GO_Central
Keywords - Cellular componenti
Nucleus, SpliceosomePathology & Biotechi
Organism-specific databases
DisGeNETi | 51639 |
OpenTargetsi | ENSG00000115128 |
Miscellaneous databases
Pharosi | Q9Y3B4, Tbio |
Polymorphism and mutation databases
BioMutai | SF3B6 |
DMDMi | 12585536 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000081725 | 1 – 125 | Splicing factor 3B subunit 6Add BLAST | 125 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 29 | N6-acetyllysine; alternateCombined sources | 1 | |
Cross-linki | 29 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources | ||
Modified residuei | 41 | N6-acetyllysineCombined sources | 1 |
Keywords - PTMi
Acetylation, Isopeptide bond, Ubl conjugationProteomic databases
EPDi | Q9Y3B4 |
jPOSTi | Q9Y3B4 |
MassIVEi | Q9Y3B4 |
MaxQBi | Q9Y3B4 |
PaxDbi | Q9Y3B4 |
PeptideAtlasi | Q9Y3B4 |
PRIDEi | Q9Y3B4 |
ProteomicsDBi | 86002 |
TopDownProteomicsi | Q9Y3B4 |
PTM databases
iPTMneti | Q9Y3B4 |
PhosphoSitePlusi | Q9Y3B4 |
SwissPalmi | Q9Y3B4 |
Expressioni
Gene expression databases
Bgeei | ENSG00000115128, Expressed in metanephros and 211 other tissues |
Genevisiblei | Q9Y3B4, HS |
Organism-specific databases
HPAi | ENSG00000115128, 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:16432215, PubMed:27720643, PubMed:28541300). Within the SF3B complex interacts directly with SF3B1 (PubMed:21062891, PubMed:16432215, Ref. 20). 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).
8 PublicationsBinary interactionsi
Q9Y3B4
With | #Exp. | IntAct |
---|---|---|
SF3B1 - isoform 1 [O75533-1] | 3 | EBI-1046261,EBI-15565798 |
Protein-protein interaction databases
BioGRIDi | 119651, 103 interactors |
CORUMi | Q9Y3B4 |
DIPi | DIP-44132N |
IntActi | Q9Y3B4, 36 interactors |
MINTi | Q9Y3B4 |
STRINGi | 9606.ENSP00000233468 |
Miscellaneous databases
RNActi | Q9Y3B4, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
BMRBi | Q9Y3B4 |
SMRi | Q9Y3B4 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9Y3B4 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 19 – 94 | RRMPROSITE-ProRule annotationAdd BLAST | 76 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 16 – 29 | Interaction with pre-mRNA branch siteAdd BLAST | 14 |
Sequence similaritiesi
Belongs to the SF3B6 family.Curated
Phylogenomic databases
eggNOGi | KOG0114, Eukaryota |
GeneTreei | ENSGT00390000005908 |
HOGENOMi | CLU_012062_25_2_1 |
InParanoidi | Q9Y3B4 |
OMAi | VNRVLFV |
OrthoDBi | 1603846at2759 |
PhylomeDBi | Q9Y3B4 |
Family and domain databases
CDDi | cd12241, RRM_SF3B14, 1 hit |
DisProti | DP01458 |
Gene3Di | 3.30.70.330, 1 hit |
IDEALi | IID00229 |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom IPR034150, SF3B6_RRM |
Pfami | View protein in Pfam PF00076, RRM_1, 1 hit |
SMARTi | View protein in SMART SM00360, RRM, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 1 hit |
i Sequence
Sequence statusi: Complete.
Q9Y3B4-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MAMQAAKRAN IRLPPEVNRI LYIRNLPYKI TAEEMYDIFG KYGPIRQIRV
60 70 80 90 100
GNTPETRGTA YVVYEDIFDA KNACDHLSGF NVCNRYLVVL YYNANRAFQK
110 120
MDTKKKEEQL KLLKEKYGIN TDPPK
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF401310 mRNA Translation: AAK94041.1 AF151868 mRNA Translation: AAD34105.1 AF161523 mRNA Translation: AAF29138.1 AF184213 mRNA Translation: AAG09698.1 AK311908 mRNA Translation: BAG34849.1 AC008073 Genomic DNA Translation: AAY14664.1 CH471053 Genomic DNA Translation: EAX00767.1 BC015463 mRNA Translation: AAH15463.1 |
CCDSi | CCDS1707.1 |
RefSeqi | NP_057131.1, NM_016047.3 |
Genome annotation databases
Ensembli | ENST00000233468; ENSP00000233468; ENSG00000115128 |
GeneIDi | 51639 |
KEGGi | hsa:51639 |
UCSCi | uc002rev.4, human |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF401310 mRNA Translation: AAK94041.1 AF151868 mRNA Translation: AAD34105.1 AF161523 mRNA Translation: AAF29138.1 AF184213 mRNA Translation: AAG09698.1 AK311908 mRNA Translation: BAG34849.1 AC008073 Genomic DNA Translation: AAY14664.1 CH471053 Genomic DNA Translation: EAX00767.1 BC015463 mRNA Translation: AAH15463.1 |
CCDSi | CCDS1707.1 |
RefSeqi | NP_057131.1, NM_016047.3 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2F9D | X-ray | 2.50 | A/B | 1-125 | [»] | |
2F9J | X-ray | 3.00 | A/B | 1-125 | [»] | |
2FHO | NMR | - | B | 8-93 | [»] | |
3LQV | X-ray | 2.38 | A/B | 11-125 | [»] | |
5Z56 | electron microscopy | 5.10 | 5 | 1-125 | [»] | |
5Z57 | electron microscopy | 6.50 | 5 | 1-125 | [»] | |
5Z58 | electron microscopy | 4.90 | 5 | 1-125 | [»] | |
6AH0 | electron microscopy | 5.70 | 5 | 1-125 | [»] | |
6FF4 | electron microscopy | 16.00 | z | 1-125 | [»] | |
6FF7 | electron microscopy | 4.50 | N/z | 1-125 | [»] | |
6Y53 | electron microscopy | 7.10 | z | 1-125 | [»] | |
6Y5Q | electron microscopy | 7.10 | z | 1-125 | [»] | |
BMRBi | Q9Y3B4 | |||||
SMRi | Q9Y3B4 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 119651, 103 interactors |
CORUMi | Q9Y3B4 |
DIPi | DIP-44132N |
IntActi | Q9Y3B4, 36 interactors |
MINTi | Q9Y3B4 |
STRINGi | 9606.ENSP00000233468 |
PTM databases
iPTMneti | Q9Y3B4 |
PhosphoSitePlusi | Q9Y3B4 |
SwissPalmi | Q9Y3B4 |
Polymorphism and mutation databases
BioMutai | SF3B6 |
DMDMi | 12585536 |
Proteomic databases
EPDi | Q9Y3B4 |
jPOSTi | Q9Y3B4 |
MassIVEi | Q9Y3B4 |
MaxQBi | Q9Y3B4 |
PaxDbi | Q9Y3B4 |
PeptideAtlasi | Q9Y3B4 |
PRIDEi | Q9Y3B4 |
ProteomicsDBi | 86002 |
TopDownProteomicsi | Q9Y3B4 |
Protocols and materials databases
Antibodypediai | 27422, 156 antibodies |
DNASUi | 51639 |
Genome annotation databases
Ensembli | ENST00000233468; ENSP00000233468; ENSG00000115128 |
GeneIDi | 51639 |
KEGGi | hsa:51639 |
UCSCi | uc002rev.4, human |
Organism-specific databases
CTDi | 51639 |
DisGeNETi | 51639 |
EuPathDBi | HostDB:ENSG00000115128.6 |
GeneCardsi | SF3B6 |
HGNCi | HGNC:30096, SF3B6 |
HPAi | ENSG00000115128, Low tissue specificity |
MIMi | 607835, gene |
neXtProti | NX_Q9Y3B4 |
OpenTargetsi | ENSG00000115128 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG0114, Eukaryota |
GeneTreei | ENSGT00390000005908 |
HOGENOMi | CLU_012062_25_2_1 |
InParanoidi | Q9Y3B4 |
OMAi | VNRVLFV |
OrthoDBi | 1603846at2759 |
PhylomeDBi | Q9Y3B4 |
Enzyme and pathway databases
PathwayCommonsi | Q9Y3B4 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
Miscellaneous databases
BioGRID-ORCSi | 51639, 670 hits in 822 CRISPR screens |
ChiTaRSi | SF3B6, human |
EvolutionaryTracei | Q9Y3B4 |
GeneWikii | SF3B14 |
GenomeRNAii | 51639 |
Pharosi | Q9Y3B4, Tbio |
PROi | PR:Q9Y3B4 |
RNActi | Q9Y3B4, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000115128, Expressed in metanephros and 211 other tissues |
Genevisiblei | Q9Y3B4, HS |
Family and domain databases
CDDi | cd12241, RRM_SF3B14, 1 hit |
DisProti | DP01458 |
Gene3Di | 3.30.70.330, 1 hit |
IDEALi | IID00229 |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom IPR034150, SF3B6_RRM |
Pfami | View protein in Pfam PF00076, RRM_1, 1 hit |
SMARTi | View protein in SMART SM00360, RRM, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | SF3B6_HUMAN | |
Accessioni | Q9Y3B4Primary (citable) accession number: Q9Y3B4 Secondary accession number(s): Q53TM1 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | January 24, 2001 |
Last sequence update: | November 1, 1999 | |
Last modified: | December 2, 2020 | |
This is version 189 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
- 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 - Human chromosome 2
Human chromosome 2: entries, gene names and cross-references to MIM