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

Gene ID: 22938, updated on 9-Dec-2024

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; AllianceGenome:HGNC:16696
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
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Genomic context

See SNW1 in Genome Data Viewer
Location:
14q24.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77717599..77761156, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71926934..71971187, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78183942..78227499, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8810 Neighboring gene zinc finger MYND-type containing 19 pseudogene 1 Neighboring gene SRA stem-loop interacting RNA binding protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78226689-78227463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78228238-78229012 Neighboring gene SLIRP overlapping transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78257054-78257970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78265777-78266315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78266316-78266854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8813 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78268449-78269288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8814 Neighboring gene aarF domain containing kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78379195-78379710 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

EBI GWAS Catalog

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

Clone Names

  • MGC119379

Gene Ontology Provided by GOA

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

NEW Try the new Transcript table

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
    B4DEG7, 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
    A8K8A9, Q13483, Q13573, Q32N03, Q5D0D6
    UniProtKB/TrEMBL
    Q6I9S2
    Related
    ENSP00000261531.8, ENST00000261531.12
    Conserved Domains (1) summary
    pfam02731
    Location:178334
    SKIP_SNW; SKIP/SNW domain

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

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_047431112.1XP_047287068.1  SNW domain-containing protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71926934..71971187 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375608.1XP_054231583.1  SNW domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    A8K8A9, Q13483, Q13573, Q32N03, Q5D0D6
    UniProtKB/TrEMBL
    Q6I9S2
  2. XM_054375609.1XP_054231584.1  SNW domain-containing protein 1 isoform X1