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SFSWAP splicing factor SWAP [ Homo sapiens (human) ]

Gene ID: 6433, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131711090..131799738)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131753414..131843835)
105.20220307 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 (49) 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)

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

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_2023_10

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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