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

Gene ID: 6431, updated on 8-May-2016
Official Symbol
SRSF6provided by HGNC
Official Full Name
serine/arginine-rich splicing factor 6provided by HGNC
Primary source
HGNC:HGNC:10788
See related
Ensembl:ENSG00000124193 HPRD:09054; MIM:601944; Vega:OTTHUMG00000032502
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]
Orthologs
Location:
20q12-q13.1
Exon count:
7
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 20 NC_000020.11 (43457864..43463605)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42086504..42092245)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase A pseudogene 21 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 pseudogene 1 Neighboring gene l(3)mbt-like 1 (Drosophila) Neighboring gene SGK2, serine/threonine kinase 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Herpes simplex infection, organism-specific biosystem (from KEGG)
    Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Herpes simplex infection, conserved biosystem (from KEGG)
    Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...
  • mRNA processing, organism-specific biosystem (from WikiPathways)
    mRNA processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC5045, FLJ08061

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
pre-mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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

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

  1. NG_029906.1 RefSeqGene

    Range
    5001..10742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006275.5NP_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
    Q13247
    Related
    ENSP00000244020, OTTHUMP00000031020, ENST00000244020, OTTHUMT00000079292
    Conserved Domains (3) summary
    smart00360
    Location:367
    RRM; RNA recognition motif
    cd12596
    Location:372
    RRM1_SRSF6; RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)
    cd12600
    Location:110181
    RRM2_SRSF4_like; RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

RNA

  1. NR_034009.1 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p2 Primary Assembly

    Range
    43457864..43463605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_936608.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018931.2 Alternate CHM1_1.1

    Range
    41990350..41996091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)