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SNW1 SNW domain containing 1 [ Homo sapiens (human) ]

Gene ID: 22938, updated on 1-Aug-2020

Summary

Official Symbol
SNW1provided by HGNC
Official Full Name
SNW domain containing 1provided by HGNC
Primary source
HGNC:HGNC:16696
See related
Ensembl:ENSG00000100603 MIM:603055
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
Bx42; SKIP; FUN20; Prp45; SKIIP; SKIP1; PRPF45; NCOA-62
Summary
This gene, a member of the SNW gene family, encodes a coactivator that enhances transcription from some Pol II promoters. This coactivator can bind to the ligand-binding domain of the vitamin D receptor and to retinoid receptors to enhance vitamin D-, retinoic acid-, estrogen-, and glucocorticoid-mediated gene expression. It can also function as a splicing factor by interacting with poly(A)-binding protein 2 to directly control the expression of muscle-specific genes at the transcriptional level. Finally, the protein may be involved in oncogenesis since it interacts with a region of SKI oncoproteins that is required for transforming activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in bone marrow (RPKM 34.9), testis (RPKM 33.4) and 25 other tissues See more
Orthologs

Genomic context

See SNW1 in Genome Data Viewer
Location:
14q24.3
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (77717599..77761156, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78183942..78227542, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene zinc finger MYND-type containing 19 pseudogene 1 Neighboring gene SRA stem-loop interacting RNA binding protein Neighboring gene chromosome 14 open reading frame 178 Neighboring gene aarF domain containing kinase 1 Neighboring gene uncharacterized LOC105370581

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of SNW domain containing 1 (SNW1) 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
Tat tat SKIP is required for Tat transactivation in vivo and stimulates HIV-1 transcription elongation by associating with CycT1:CDK9 (P-TEFb) and Tat:P-TEFb complexes both in nuclear extracts and in recombinant Tat:P-TEFb:TAR RNA complexes in vitro PubMed
tat SKIP recruits c-Myc and TRRAP to the HIV-1 Tat-activated LTR promoter. Knockdown of SKIP has no effect on the recruitment of Tat, CycT1, RNAPII, or Ser2P and Ser5P levels at the HIV-1 promoter PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human SNW domain containing 1 (SNW1) at amino acid residues 150-151 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119379

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Notch binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA binding HDA PubMed 
SMAD binding IDA
Inferred from Direct Assay
more info
PubMed 
androgen receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
nuclear hormone receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoic acid receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
vitamin D receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Notch signaling pathway TAS
Traceable Author Statement
more info
 
cellular response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation by host of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation by host of viral transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of Notch signaling pathway TAS
Traceable Author Statement
more info
 
positive regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of neurogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
positive regulation of transcription of Notch receptor target TAS
Traceable Author Statement
more info
 
positive regulation of transforming growth factor beta receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
regulation of retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
regulation of vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with cyclin/CDK positive transcription elongation factor complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
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
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
SNW domain-containing protein 1
Names
SKI interacting protein
homolog of Drosophila BX42
nuclear protein SkiP
nuclear receptor coactivator NCoA-62
nuclear receptor coactivator, 62-kD
ski-interacting protein

NCBI Reference Sequences (RefSeq)

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_001318844.2NP_001305773.1  SNW domain-containing protein 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC008372
    Consensus CDS
    CCDS81830.1
    UniProtKB/TrEMBL
    G3V3A4
    Related
    ENSP00000451129.1, ENST00000555761.5
    Conserved Domains (1) summary
    pfam02731
    Location:178334
    SKIP_SNW; SKIP/SNW domain
  2. NM_012245.3NP_036377.1  SNW domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_036377.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC008372
    Consensus CDS
    CCDS9867.1
    UniProtKB/Swiss-Prot
    Q13573
    Related
    ENSP00000261531.7, ENST00000261531.11
    Conserved Domains (1) summary
    pfam02731
    Location:178334
    SKIP_SNW; SKIP/SNW domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    77717599..77761156 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005267413.4XP_005267470.1  SNW domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    pfam02731
    Location:178334
    SKIP_SNW; SKIP/SNW domain
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