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    SFSWAP splicing factor SWAP [ Homo sapiens (human) ]

    Gene ID: 6433, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SFSWAPprovided by HGNC
    Official Full Name
    splicing factor SWAPprovided by HGNC
    Primary source
    HGNC:HGNC:10790
    See related
    Ensembl:ENSG00000061936 MIM:601945; AllianceGenome:HGNC:10790
    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
    SWAP; SFRS8
    Summary
    This gene encodes a human homolog of Drosophila splicing regulatory protein. This gene autoregulates its expression by control of splicing of its first two introns. In addition, it also regulates the splicing of fibronectin and CD45 genes. Two transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012]
    Expression
    Ubiquitous expression in bone marrow (RPKM 11.1), spleen (RPKM 9.4) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See SFSWAP in Genome Data Viewer
    Location:
    12q24.33
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131711090..131799738)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131753414..131843835)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (132195635..132284283)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132156613-132157112 Neighboring gene uncharacterized LOC105370087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7369 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:132204952-132206151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132213273-132213837 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132216488-132217157 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132217158-132217826 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:132221080-132222279 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132257981-132258606 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132258607-132259231 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:132269252-132270451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132271907-132272407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132280316-132281138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132281963-132282784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132284875-132285724 Neighboring gene RNA, 5S ribosomal pseudogene 378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132295853-132296798 Neighboring gene RNA, U6 small nuclear 1017, pseudogene

    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. Significant linkage to chromosome 12q24.32-q24.33 and identification of SFRS8 as a possible asthma susceptibility gene. Brasch-Andersen C, et al. Thorax, 2006 Oct. PMID 16738036, Free PMC Article
    2. Conservation of regulated alternative splicing and identification of functional domains in vertebrate homologs to the Drosophila splicing regulator, suppressor-of-white-apricot. Denhez F, et al. J Biol Chem, 1994 Jun 10. PMID 8206918
    3. The mammalian homolog of suppressor-of-white-apricot regulates alternative mRNA splicing of CD45 exon 4 and fibronectin IIICS. Sarkissian M, et al. J Biol Chem, 1996 Dec 6. PMID 8940107
    4. Identification and characterization of essential genes in the human genome. Wang T, et al. Science, 2015 Nov 27. PMID 26472758, Free PMC Article
    5. The candidate splicing factor Sfswap regulates growth and patterning of inner ear sensory organs. Moayedi Y, et al. PLoS Genet, 2014 Jan. PMID 24391519, Free PMC Article

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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)

    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

    Clone Names

    • MGC167082

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in alternative mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA 5'-splice site recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    splicing factor, suppressor of white-apricot homolog
    Names
    splicing factor SWAP homolog
    splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)
    splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)
    splicing factor, suppressor of white-apricot family
    suppressor of white apricot protein homolog

    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_001261411.2 → NP_001248340.1  splicing factor, suppressor of white-apricot homolog isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC117500, AC131009
      Consensus CDS
      CCDS58290.1
      UniProtKB/Swiss-Prot
      Q12872
      Related
      ENSP00000437738.1, ENST00000541286.5
      Conserved Domains (3) summary
      smart00648
      Location:209 → 262
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam01346
      Location:637 → 677
      FKBP_N; Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
      pfam09750
      Location:35 → 155
      DRY_EERY; Alternative splicing regulator

    2. NM_004592.4 → NP_004583.2  splicing factor, suppressor of white-apricot homolog isoform 2

      See identical proteins and their annotated locations for NP_004583.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC117500, AC131009
      Consensus CDS
      CCDS9273.1
      UniProtKB/Swiss-Prot
      B2RN45, B7ZM97, F5H6B8, Q12872, Q6PJF7
      Related
      ENSP00000261674.4, ENST00000261674.9
      Conserved Domains (3) summary
      smart00648
      Location:209 → 262
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam01346
      Location:637 → 677
      FKBP_N; Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
      pfam09750
      Location:35 → 155
      DRY_EERY; Alternative splicing regulator

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      131711090..131799738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024449125.1 → XP_024304893.1  splicing factor, suppressor of white-apricot homolog isoform X2

      Conserved Domains (2) summary
      smart00648
      Location:83 → 136
      SWAP; Suppressor-of-White-APricot splicing regulator
      cl00368
      Location:511 → 592
      Ribosomal_S16; Ribosomal protein S16

    2. XM_047429327.1 → XP_047285283.1  splicing factor, suppressor of white-apricot homolog isoform X5

    3. XM_047429328.1 → XP_047285284.1  splicing factor, suppressor of white-apricot homolog isoform X6

    4. XM_011538653.1 → XP_011536955.1  splicing factor, suppressor of white-apricot homolog isoform X1

      Conserved Domains (3) summary
      PRK12495
      Location:504 → 618
      PRK12495; hypothetical protein; Provisional
      smart00648
      Location:209 → 262
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam09750
      Location:35 → 155
      DRY_EERY; Alternative splicing regulator

    5. XM_017019798.1 → XP_016875287.1  splicing factor, suppressor of white-apricot homolog isoform X3

    6. XM_011538655.3 → XP_011536957.1  splicing factor, suppressor of white-apricot homolog isoform X4

      Conserved Domains (3) summary
      smart00648
      Location:209 → 262
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam01346
      Location:637 → 677
      FKBP_N; Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
      pfam09750
      Location:35 → 155
      DRY_EERY; Alternative splicing regulator

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      131753414..131843835
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372862.1 → XP_054228837.1  splicing factor, suppressor of white-apricot homolog isoform X2

    2. XM_054372866.1 → XP_054228841.1  splicing factor, suppressor of white-apricot homolog isoform X6

    3. XM_054372865.1 → XP_054228840.1  splicing factor, suppressor of white-apricot homolog isoform X5

    4. XM_054372861.1 → XP_054228836.1  splicing factor, suppressor of white-apricot homolog isoform X1

    5. XM_054372863.1 → XP_054228838.1  splicing factor, suppressor of white-apricot homolog isoform X3

    6. XM_054372864.1 → XP_054228839.1  splicing factor, suppressor of white-apricot homolog isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152235.1: Suppressed sequence

      Description
      NM_152235.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12872.3 GenPept UniProtKB/Swiss-Prot:Q12872

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