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

Summary

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, Oct 2024]
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

Location:: 19q13.33

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (49640465..49658642)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (52640497..52658671)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (50145466..50161899)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SCAF1 drives the compositional diversity of mammalian respirasomes.
Title: SCAF1 drives the compositional diversity of mammalian respirasomes.
In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.
Title: In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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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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)

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

49640465..49658642

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011527194.4 → XP_011525496.1 splicing factor, arginine/serine-rich 19 isoform X1
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
XM_017027083.3 → XP_016882572.1 splicing factor, arginine/serine-rich 19 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

52640497..52658671

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321632.1 → XP_054177607.1 splicing factor, arginine/serine-rich 19 isoform X1
XM_054321630.1 → XP_054177605.1 splicing factor, arginine/serine-rich 19 isoform X2
XM_054321631.1 → XP_054177606.1 splicing factor, arginine/serine-rich 19 isoform X2
XM_054321633.1 → XP_054177608.1 splicing factor, arginine/serine-rich 19 isoform X3