SRSF6 serine and arginine rich splicing factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SRSF6provided by HGNC
Official Full Name: serine and arginine rich splicing factor 6provided by HGNC
Primary source: HGNC:HGNC:10788
See related: Ensembl:ENSG00000124193 MIM:601944; AllianceGenome:HGNC:10788
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: B52; SFRS6; SRP55; HEL-S-91
Summary: The protein encoded by this gene is involved in mRNA splicing and may play a role in the determination of alternative splicing. The encoded nuclear protein belongs to the splicing factor SR family and has been shown to bind with and modulate another member of the family, SFRS12. Alternative splicing results in multiple transcript variants. In addition, two pseudogenes, one on chromosome 17 and the other on the X chromosome, have been found for this gene.[provided by RefSeq, Sep 2010]
Expression: Ubiquitous expression in bone marrow (RPKM 64.4), prostate (RPKM 51.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (43457896..43464243)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (45191165..45197503)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (42086536..42092883)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genetic compensation response could exist in colorectal cancer: UPF3A upregulates the oncogenic homologue gene SRSF3 expression corresponding to SRSF6 to promote colorectal cancer metastasis.
Title: Genetic compensation response could exist in colorectal cancer: UPF3A upregulates the oncogenic homologue gene SRSF3 expression corresponding to SRSF6 to promote colorectal cancer metastasis.
Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia.
Title: Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia.
A candidate gene study reveals association between a variant of the SRp55 splicing factor gene and systemic sclerosis.
Title: A candidate gene study reveals association between a variant of the SRp55 splicing factor gene and systemic sclerosis.
DRAK2 aggravates nonalcoholic fatty liver disease progression through SRSF6-associated RNA alternative splicing.
Title: DRAK2 aggravates nonalcoholic fatty liver disease progression through SRSF6-associated RNA alternative splicing.
Splicing factor SRSF6 mediates pleural fibrosis.
Title: Splicing factor SRSF6 mediates pleural fibrosis.
Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia.
Title: Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia.
Relative strength of 5' splice-site strength defines functions of SRSF2 and SRSF6 in alternative splicing of Bcl-x pre-mRNA.
Title: Relative strength of 5' splice-site strength defines functions of SRSF2 and SRSF6 in alternative splicing of Bcl-x pre-mRNA.
The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic beta-cells.
Title: The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells.
LncRNA CRNDE attenuates chemoresistance in gastric cancer via SRSF6-regulated alternative splicing of PICALM.
Title: LncRNA CRNDE attenuates chemoresistance in gastric cancer via SRSF6-regulated alternative splicing of PICALM.
SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells.
Title: SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells.

Submit: New GeneRIF Correction See all GeneRIFs (34)

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of serine/arginine-rich splicing factor 6 (SRSF6) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	SRSF6 expression inhibits inclusion of exons 4cab and 5 into viral Rev and Nef-mRNAs by shifting a viral splice acceptor selection from 3'ss A5 to 3'ss A3 usage, leading to decreased levels of Rev and Nef proteins	PubMed
Pr55(Gag)	gag	SR proteins, particularly SRp40 and SRp55, increase HIV-1 Gag translation from unspliced viral RNA. The second RNA recognition motif and the arginine-serine (RS) domain are determinants of SR protein activity	PubMed
Rev	rev	SRSF6 expression inhibits inclusion of exons 4cab and 5 into viral Rev and Nef-mRNAs by shifting a viral splice acceptor selection from 3'ss A5 to 3'ss A3 usage, leading to decreased levels of Rev and Nef proteins	PubMed
Tat	tat	SRSF2 and SRSF6 cooperatively activate HIV-1 Tat-specific 3'ss A3 site, either through two separate required mechanisms or by stabilizing each other on their respective target sequences	PubMed
capsid	gag	SRp55 induces production of extracellular p24gag from a rev-defective HIV-1 provirus	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

SGC32867 (e-PCR)
- UniSTS:45591

RH47503 (e-PCR)
- UniSTS:62573

SFRS6_8615 (e-PCR)
- UniSTS:467879

RH18029 (e-PCR)
- UniSTS:59111

NIB331 (e-PCR)
- UniSTS:63978

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables pre-mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in alternative mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA splice site recognition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of keratinocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of type B pancreatic cell apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of epithelial cell proliferation involved in lung morphogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of keratinocyte proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of wound healing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to insulin	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in nuclear speck	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: serine/arginine-rich splicing factor 6

Names: SR splicing factor 6; epididymis secretory protein Li 91; pre-mRNA-splicing factor SRP55; splicing factor, arginine/serine-rich, 55 kDa

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.

Genomic

NG_029906.1 RefSeqGene

Range

5033..11380

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006275.6 → NP_006266.2 serine/arginine-rich splicing factor 6

See identical proteins and their annotated locations for NP_006266.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter, protein-coding transcript.

Source sequence(s)

AL031681, BC006832, BM830876, DC306805

Consensus CDS

CCDS13318.1

UniProtKB/Swiss-Prot

B7Z6J3, E1P5W6, Q13244, Q13245, Q13247, Q96J06, Q9UJB8, Q9Y3N7

Related

ENSP00000244020.3, ENST00000244020.5

Conserved Domains (2) summary

cd12596
Location:1 → 72

RRM1_SRSF6; RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

cd12766
Location:110 → 182

RRM2_SRSF6; RNA recognition motif 2 (RRM2) found found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

RNA

NR_034009.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate exon the coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK300411, AL031681, AV704620, DC306805