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Protein

Splicing factor 3B subunit 6

Gene

SF3B6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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

GO - Biological processi

  • blastocyst formation Source: Ensembl
  • mRNA splicing, via spliceosome Source: GO_Central

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor 3B subunit 6
Alternative 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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000115128.6
HGNCiHGNC:30096 SF3B6
MIMi607835 gene
neXtProtiNX_Q9Y3B4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi51639
OpenTargetsiENSG00000115128

Polymorphism and mutation databases

BioMutaiSF3B14
DMDMi12585536

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000817251 – 125Splicing factor 3B subunit 6Add BLAST125

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei29N6-acetyllysine; alternateCombined sources1
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei41N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ9Y3B4
MaxQBiQ9Y3B4
PaxDbiQ9Y3B4
PeptideAtlasiQ9Y3B4
PRIDEiQ9Y3B4
ProteomicsDBi86002
TopDownProteomicsiQ9Y3B4

PTM databases

iPTMnetiQ9Y3B4
PhosphoSitePlusiQ9Y3B4
SwissPalmiQ9Y3B4

Expressioni

Gene expression databases

BgeeiENSG00000115128 Expressed in 197 organ(s), highest expression level in metanephros
GenevisibleiQ9Y3B4 HS

Organism-specific databases

HPAiHPA034829
HPA034830

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 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SF3B1O75533-13EBI-1046261,EBI-15565798

Protein-protein interaction databases

BioGridi119651, 78 interactors
CORUMiQ9Y3B4
DIPiDIP-44132N
IntActiQ9Y3B4, 23 interactors
MINTiQ9Y3B4
STRINGi9606.ENSP00000233468

Structurei

Secondary structure

1125
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9Y3B4
SMRiQ9Y3B4
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y3B4

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini19 – 94RRMPROSITE-ProRule annotationAdd BLAST76

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni16 – 29Interaction with pre-mRNA branch siteAdd BLAST14

Sequence similaritiesi

Belongs to the SF3B6 family.Curated

Phylogenomic databases

eggNOGiKOG0114 Eukaryota
ENOG4111IHX LUCA
GeneTreeiENSGT00390000005908
HOGENOMiHOG000276232
HOVERGENiHBG039634
InParanoidiQ9Y3B4
KOiK12833
OMAiVNRVLFV
OrthoDBiEOG091G0RTZ
PhylomeDBiQ9Y3B4

Family and domain databases

CDDicd12241 RRM_SF3B14, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
IPR034150 SF3B14_RRM
PANTHERiPTHR12785:SF7 PTHR12785:SF7, 1 hit
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequencei

Sequence statusi: Complete.

Q9Y3B4-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:125
Mass (Da):14,585
Last modified:November 1, 1999 - v1
Checksum:iA1439DACB78A3208
GO

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
CCDSiCCDS1707.1
RefSeqiNP_057131.1, NM_016047.3
UniGeneiHs.177861

Genome annotation databases

EnsembliENST00000233468; ENSP00000233468; ENSG00000115128
GeneIDi51639
KEGGihsa:51639
UCSCiuc002rev.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
CCDSiCCDS1707.1
RefSeqiNP_057131.1, NM_016047.3
UniGeneiHs.177861

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2F9DX-ray2.50A/B1-125[»]
2F9JX-ray3.00A/B1-125[»]
2FHONMR-B8-93[»]
3LQVX-ray2.38A/B11-125[»]
5Z56electron microscopy5.1051-125[»]
5Z57electron microscopy6.5051-125[»]
5Z58electron microscopy4.9051-125[»]
6FF4electron microscopy16.00z1-125[»]
ProteinModelPortaliQ9Y3B4
SMRiQ9Y3B4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119651, 78 interactors
CORUMiQ9Y3B4
DIPiDIP-44132N
IntActiQ9Y3B4, 23 interactors
MINTiQ9Y3B4
STRINGi9606.ENSP00000233468

PTM databases

iPTMnetiQ9Y3B4
PhosphoSitePlusiQ9Y3B4
SwissPalmiQ9Y3B4

Polymorphism and mutation databases

BioMutaiSF3B14
DMDMi12585536

Proteomic databases

EPDiQ9Y3B4
MaxQBiQ9Y3B4
PaxDbiQ9Y3B4
PeptideAtlasiQ9Y3B4
PRIDEiQ9Y3B4
ProteomicsDBi86002
TopDownProteomicsiQ9Y3B4

Protocols and materials databases

DNASUi51639
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000233468; ENSP00000233468; ENSG00000115128
GeneIDi51639
KEGGihsa:51639
UCSCiuc002rev.4 human

Organism-specific databases

CTDi51639
DisGeNETi51639
EuPathDBiHostDB:ENSG00000115128.6
GeneCardsiSF3B6
HGNCiHGNC:30096 SF3B6
HPAiHPA034829
HPA034830
MIMi607835 gene
neXtProtiNX_Q9Y3B4
OpenTargetsiENSG00000115128
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0114 Eukaryota
ENOG4111IHX LUCA
GeneTreeiENSGT00390000005908
HOGENOMiHOG000276232
HOVERGENiHBG039634
InParanoidiQ9Y3B4
KOiK12833
OMAiVNRVLFV
OrthoDBiEOG091G0RTZ
PhylomeDBiQ9Y3B4

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway

Miscellaneous databases

ChiTaRSiSF3B6 human
EvolutionaryTraceiQ9Y3B4
GeneWikiiSF3B14
GenomeRNAii51639
PROiPR:Q9Y3B4
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115128 Expressed in 197 organ(s), highest expression level in metanephros
GenevisibleiQ9Y3B4 HS

Family and domain databases

CDDicd12241 RRM_SF3B14, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
IPR034150 SF3B14_RRM
PANTHERiPTHR12785:SF7 PTHR12785:SF7, 1 hit
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSF3B6_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3B4
Secondary accession number(s): Q53TM1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 24, 2001
Last sequence update: November 1, 1999
Last modified: November 7, 2018
This is version 172 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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