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

Gene ID: 58506, updated on 5-Mar-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
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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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