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Protein

Splicing factor 3B subunit 4

Gene

SF3B4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. 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 Publications

GO - Molecular functioni

  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA processing Source: ProtInc
  • mRNA splicing, via spliceosome Source: Reactome
  • positive regulation of mRNA splicing, via spliceosome Source: Ensembl
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: ProtInc

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 4
Alternative name(s):
Pre-mRNA-splicing factor SF3b 49 kDa subunit
Spliceosome-associated protein 49
Short name:
SAP 49
Gene namesi
Name:SF3B4
Synonyms:SAP49
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000143368.9.
HGNCiHGNC:10771. SF3B4.

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

Involvement in diseasei

Acrofacial dysostosis 1, Nager type (AFD1)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of acrofacial dysostosis, a group of disorders which are characterized by malformation of the craniofacial skeleton and the limbs. The major facial features of AFD1 include downslanted palpebral fissures, midface retrusion, and micrognathia, the latter of which often requires the placement of a tracheostomy in early childhood. Limb defects typically involve the anterior (radial) elements of the upper limbs and manifest as small or absent thumbs, triphalangeal thumbs, radial hyoplasia or aplasia, and radioulnar synostosis. Phocomelia of the upper limbs and, occasionally, lower-limb defects have also been reported.
See also OMIM:154400

Organism-specific databases

DisGeNETi10262.
MalaCardsiSF3B4.
MIMi154400. phenotype.
OpenTargetsiENSG00000143368.
Orphaneti245. Nager syndrome.
PharmGKBiPA35689.

Polymorphism and mutation databases

BioMutaiSF3B4.
DMDMi2500587.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00000819552 – 424Splicing factor 3B subunit 4Add BLAST423

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1
Modified residuei56PhosphotyrosineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ15427.
MaxQBiQ15427.
PaxDbiQ15427.
PeptideAtlasiQ15427.
PRIDEiQ15427.

PTM databases

iPTMnetiQ15427.
PhosphoSitePlusiQ15427.
SwissPalmiQ15427.

Expressioni

Gene expression databases

BgeeiENSG00000143368.
CleanExiHS_SF3B4.
ExpressionAtlasiQ15427. baseline and differential.
GenevisibleiQ15427. HS.

Organism-specific databases

HPAiHPA028578.
HPA064660.

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 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi115554. 111 interactors.
CORUMiQ15427.
IntActiQ15427. 62 interactors.
MINTiMINT-1032702.
STRINGi9606.ENSP00000271628.

Structurei

Secondary structure

1424
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni11 – 13Combined sources3
Beta strandi14 – 18Combined sources5
Helixi26 – 34Combined sources9
Beta strandi39 – 43Combined sources5
Beta strandi48 – 50Combined sources3
Beta strandi57 – 63Combined sources7
Helixi64 – 73Combined sources10
Beta strandi74 – 76Combined sources3
Beta strandi85 – 88Combined sources4
Turni89 – 92Combined sources4
Beta strandi102 – 105Combined sources4
Helixi113 – 121Combined sources9
Beta strandi126 – 128Combined sources3
Turni136 – 138Combined sources3
Beta strandi143 – 151Combined sources9
Helixi152 – 160Combined sources9
Turni161 – 164Combined sources4
Beta strandi173 – 177Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X5TNMR-A102-184[»]
5GVQNMR-A5-96[»]
ProteinModelPortaliQ15427.
SMRiQ15427.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ15427.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini13 – 91RRM 1PROSITE-ProRule annotationAdd BLAST79
Domaini100 – 179RRM 2PROSITE-ProRule annotationAdd BLAST80

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi215 – 218Poly-Pro4
Compositional biasi262 – 268Poly-Pro7

Sequence similaritiesi

Belongs to the SF3B4 family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0131. Eukaryota.
ENOG410XPT4. LUCA.
GeneTreeiENSGT00870000136537.
HOGENOMiHOG000200535.
HOVERGENiHBG002295.
InParanoidiQ15427.
KOiK12831.
OMAiPNAWAPP.
OrthoDBiEOG091G0HAI.
PhylomeDBiQ15427.
TreeFamiTF300890.

Family and domain databases

CDDicd12334. RRM1_SF3B4. 1 hit.
cd12335. RRM2_SF3B4. 1 hit.
InterProiView protein in InterPro
IPR035979. RBD_domain_sf.
IPR000504. RRM_dom.
IPR034158. SF3B4_RRM1.
IPR034159. SF3B4_RRM2.
PfamiView protein in Pfam
PF00076. RRM_1. 2 hits.
SMARTiView protein in SMART
SM00360. RRM. 2 hits.
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiView protein in PROSITE
PS50102. RRM. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q15427-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:424
Mass (Da):44,386
Last modified:November 1, 1996 - v1
Checksum:i212472A25D3FF002
GO

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.
CCDSiCCDS72900.1.
PIRiA54964.
RefSeqiNP_005841.1. NM_005850.4.
UniGeneiHs.516160.

Genome annotation databases

EnsembliENST00000271628; ENSP00000271628; ENSG00000143368.
GeneIDi10262.
KEGGihsa:10262.
UCSCiuc001etk.3. human.

Similar proteinsi

Entry informationi

Entry nameiSF3B4_HUMAN
AccessioniPrimary (citable) accession number: Q15427
Secondary accession number(s): Q5SZ63
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: October 25, 2017
This is version 185 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. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families