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

    Gene ID: 51639, updated on 3-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (24067586..24076326, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (24102271..24111005, complement)
    RS_2024_09 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 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. Structural model of the p14/SF3b155 · branch duplex complex. Schellenberg MJ, et al. RNA, 2011 Jan. PMID 21062891, Free PMC Article
    4. 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
    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 (129) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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