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    SCAF1 SR-related CTD associated factor 1 [ Homo sapiens (human) ]

    Gene ID: 58506, updated on 5-May-2024

    Summary

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    Official Symbol
    SCAF1provided by HGNC
    Official Full Name
    SR-related CTD associated factor 1provided by HGNC
    Primary source
    HGNC:HGNC:30403
    See related
    Ensembl:ENSG00000126461 MIM:617264; AllianceGenome:HGNC:30403
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SRA1
    Summary
    Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in fat (RPKM 11.1), brain (RPKM 11.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.33
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49640465..49658642)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52640497..52658671)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50145466..50161899)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50095111-50095610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10925 Neighboring gene proline rich 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50135833-50136332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50139452-50140018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143247-50143916 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143917-50144586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50144587-50145256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10927 Neighboring gene RAS related Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50158945-50159720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50161341-50162044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10929 Neighboring gene interferon regulatory factor 3 Neighboring gene BCL2 like 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50175361-50175919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50180167-50180898 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50184019-50184183 Neighboring gene protein arginine methyltransferase 1 Neighboring gene microRNA 5088

    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. Discovery and expression analysis of novel transcripts of the human SR-related CTD-associated factor 1 (SCAF1) gene in human cancer cells using Next-Generation Sequencing. Adamopoulos PG, et al. Gene, 2018 Sep 5. PMID 29787824
    2. Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer. Leoutsakou T, et al. Biochem Biophys Res Commun, 2006 Jun 2. PMID 16631123
    3. SR-A1, a member of the human pre-mRNA splicing factor family, and its expression in colon cancer progression. Mathioudaki K, et al. Biol Chem, 2004 Sep. PMID 15493872
    4. Cloning of a gene (SR-A1), encoding for a new member of the human Ser/Arg-rich family of pre-mRNA splicing factors: overexpression in aggressive ovarian cancer. Scorilas A, et al. Br J Cancer, 2001 Jul 20. PMID 11461075, Free PMC Article
    5. Analysis of the acrolein-modified sites of apolipoprotein B-100 in LDL. Kobayashi M, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2021 Jan. PMID 32919080

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of the acrolein-modified sites of apolipoprotein B-100 in LDL.
      Title: Analysis of the acrolein-modified sites of apolipoprotein B-100 in LDL.
    2. This is the first study that examines the expression of the novel gene SR-A1 in colon cancer progression.
      Title: SR-A1, a member of the human pre-mRNA splicing factor family, and its expression in colon cancer progression.
    3. Study describes the discovery and cloning of fifteen novel splice variants of SCAF1 gene in cancer cells comprising a total of nine novel alternative splicing events between the annotated exons of the gene, producing seven novel SCAF1 transcripts with open-reading frames, and eight novel SCAF1 transcripts with premature termination codons that are likely long non-coding RNAs. Additionally, a novel 3' UTR was discovered.
      Title: Discovery and expression analysis of novel transcripts of the human SR-related CTD-associated factor 1 (SCAF1) gene in human cancer cells using Next-Generation Sequencing.
    4. This study unveils the presence of SR-A1, CD36, and LOX-1 in aortic valves and suggests potential mechanisms by which they may contribute to the pathological angiogenesis, inflammation, calcification, and lipid accumulation in AVS.
      Title: Potential pathological roles for oxidized low-density lipoprotein and scavenger receptors SR-AI, CD36, and LOX-1 in aortic valve stenosis.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    7. 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.
    8. Our results suggest that SRA1 is associated with cancer progression and may possibly be characterized as a new marker of unfavorable prognosis for ovarian cancer.
      Title: Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer.
    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

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of SR-related CTD-associated factor 1 (SCAF1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ00034

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II C-terminal domain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II C-terminal domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein domain specific binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    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, arginine/serine-rich 19
    Names
    SCAF
    SR-related C-terminal domain-associated factor 1
    SR-related and CTD-associated factor 1
    SR-related-CTD-associated factor
    serine arginine-rich pre-mRNA splicing factor SR-A1

    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_021228.3 → NP_067051.2  splicing factor, arginine/serine-rich 19

      See identical proteins and their annotated locations for NP_067051.2

      Status: VALIDATED

      Source sequence(s)
      AC011495
      Consensus CDS
      CCDS33074.1
      UniProtKB/Swiss-Prot
      Q7Z5V7, Q8WVA1, Q9H7N4, Q9NR59
      Related
      ENSP00000353769.2, ENST00000360565.8

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      49640465..49658642
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527194.4 → XP_011525496.1  splicing factor, arginine/serine-rich 19 isoform X1

    2. XM_005259122.6 → XP_005259179.1  splicing factor, arginine/serine-rich 19 isoform X2

      See identical proteins and their annotated locations for XP_005259179.1

      UniProtKB/Swiss-Prot
      Q7Z5V7, Q8WVA1, Q9H7N4, Q9NR59

    3. XM_017027083.3 → XP_016882572.1  splicing factor, arginine/serine-rich 19 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      52640497..52658671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321632.1 → XP_054177607.1  splicing factor, arginine/serine-rich 19 isoform X1

    2. XM_054321630.1 → XP_054177605.1  splicing factor, arginine/serine-rich 19 isoform X2

    3. XM_054321631.1 → XP_054177606.1  splicing factor, arginine/serine-rich 19 isoform X2

    4. XM_054321633.1 → XP_054177608.1  splicing factor, arginine/serine-rich 19 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7N4.3 GenPept UniProtKB/Swiss-Prot:Q9H7N4

    Gene LinkOut

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

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