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SF3B6 splicing factor 3b subunit 6 [ Homo sapiens (human) ]

Gene ID: 51639, updated on 5-Mar-2024

Summary

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Official Symbol
SF3B6provided by HGNC
Official Full Name
splicing factor 3b subunit 6provided by HGNC
Primary source
HGNC:HGNC:30096
See related
Ensembl:ENSG00000115128 MIM:607835; AllianceGenome:HGNC:30096
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
P14; Ht006; SAP14; SAP14a; SF3B14; CGI-110; HSPC175; SF3B14a
Summary
This gene encodes a 14 kDa protein subunit of the splicing factor 3b complex. Splicing factor 3b associates with both the U2 and U11/U12 small nuclear ribonucleoprotein complexes (U2 snRNP) of spliceosomes. This 14 kDa protein interacts directly with subunit 1 of the splicing factor 3b complex. This 14 kDa protein also interacts directly with the adenosine that carries out the first transesterification step of splicing at the pre-mRNA branch site. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 53.9), colon (RPKM 39.5) and 25 other tissues See more
Orthologs
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Genomic context

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See SF3B6 in Genome Data Viewer
Location:
2p23.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (24067586..24076326, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (24102271..24111005, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (24290456..24299196, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24238941-24239496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24239497-24240052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:24244092-24244708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24246333-24247318 Neighboring gene MFSD2 lysolipid transporter B, sphingolipid Neighboring gene FKBP prolyl isomerase 1B Neighboring gene WD repeat and coiled coil containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11225 Neighboring gene RNA, U6 small nuclear 370, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:24276709-24276900 Neighboring gene Sharpr-MPRA regulatory region 5215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:24298482-24299014 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:24299015-24299546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24305416-24306346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:24307989-24308489 Neighboring gene family with sequence similarity 228 member B Neighboring gene tumor protein p53 inducible protein 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:24317825-24319024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11228 Neighboring gene profilin family member 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC. Li J, et al. Mol Med, 2021 Aug 28. PMID 34470609, Free PMC Article
  2. Interaction between the Spliceosomal Pre-mRNA Branch Site and U2 snRNP Protein p14. Perea W, et al. Biochemistry, 2016 Feb 2. PMID 26784522
  3. SF3B14 is involved in the centrosome regulation through splicing of TUBGCP6 pre-mRNA. Kato K, et al. Biochem Biophys Res Commun, 2022 Jan 15. PMID 34954520
  4. Structural model of the p14/SF3b155 · branch duplex complex. Schellenberg MJ, et al. RNA, 2011 Jan. PMID 21062891, Free PMC Article
  5. Crystal structure of a core spliceosomal protein interface. Schellenberg MJ, et al. Proc Natl Acad Sci U S A, 2006 Jan 31. PMID 16432215, Free PMC Article

See all (109) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SF3B14 is involved in the centrosome regulation through splicing of TUBGCP6 pre-mRNA.
    Title: SF3B14 is involved in the centrosome regulation through splicing of TUBGCP6 pre-mRNA.
  2. The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC.
    Title: The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC.
  3. the p14-RNA interaction screens charges on the backbone of the branch site during spliceosome assembly.
    Title: Interaction between the Spliceosomal Pre-mRNA Branch Site and U2 snRNP Protein p14.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
  5. determined the high resolution structure of a complex between SF3b14 and a peptide derived from SF3b155 and proposed a model for recognition of the pre-mRNA branch sequence adenosine.
    Title: Crystal structure of a core spliceosomal protein interface.
  6. determined the three-dimensional structure of the human SF3b complex by single-particle electron cryomicroscopy at a resolution of less than 10 angstroms, allowing identification of protein domains with known structural folds
    Title: Molecular architecture of the multiprotein splicing factor SF3b.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables mRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in U2-type prespliceosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in blastocyst formation IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U2-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
splicing factor 3B subunit 6
Names
SF3b 14 kDa subunit
pre-mRNA branch site protein p14
spliceosome-associated protein, 14 kDa subunit
spliceosome-associated protein, 14-kDa
splicing factor 3B, 14 kDa subunit
splicing factor 3b, subunit 6, 14kDa

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_016047.4 → NP_057131.1  splicing factor 3B subunit 6

    See identical proteins and their annotated locations for NP_057131.1

    Status: REVIEWED

    Source sequence(s)
    BC015463, BG200650
    Consensus CDS
    CCDS1707.1
    UniProtKB/Swiss-Prot
    Q53TM1, Q9Y3B4
    Related
    ENSP00000233468.4, ENST00000233468.5
    Conserved Domains (1) summary
    cd12241
    Location:17 → 93
    RRM_SF3B14; RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    24067586..24076326 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    24102271..24111005 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y3B4.1 GenPept UniProtKB/Swiss-Prot:Q9Y3B4

Gene LinkOut

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