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

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: mouse all
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Genomic context

Location:: 14q24.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (77717599..77761156, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (71926934..71971187, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (78183942..78227499, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

SNW1 interacts with IKKgamma to positively regulate antiviral innate immune responses against influenza A virus infection.
Title: SNW1 interacts with IKKγ to positively regulate antiviral innate immune responses against influenza A virus infection.
Skip is essential for Notch signaling to induce Sox2 in cerebral arteriovenous malformations.
Title: Skip is essential for Notch signaling to induce Sox2 in cerebral arteriovenous malformations.
SNW1 is a unique protein previously shown to be involved in both splicing and transcription, and in this case, its role involves binding to the NF-kappaB-p-TEFb complex to facilitate transcriptional elongation of some NF-kappaB target genes.
Title: SNW1, a Novel Transcriptional Regulator of the NF-κB Pathway.
These results demonstrate that SNW1 overexpression is an independent prognostic marker in prostate cancer with potential clinical utility.
Title: SNW1 is a prognostic biomarker in prostate cancer.
SNW1 interacts with RBPJ to regulate the Notch signaling pathway in neuroblastoma
Title: SNW1 regulates Notch signaling in neuroblastoma through interacting with RBPJ.
c-Abl promotes TGF-beta-induced SKIP/Smad3 interaction.
Title: Enhancement of TGF-β-induced Smad3 activity by c-Abl-mediated tyrosine phosphorylation of its coactivator SKI-interacting protein (SKIP).
Higher SKIP expression is associated with poor prognosis in malignant pleural mesothelioma
Title: Comparison of SKIP expression in malignant pleural mesotheliomas with Ki-67 proliferation index and prognostic parameters.
Upon step 1 catalysis, Cwc25 contacts with the branch-site region, and enhanced crosslinks of Prp8 and Prp45 with nucleotides surrounding the branch-site were observed.
Title: Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes.
Rab1A regulates anterograde melanosome transport by recruiting kinesin-1 to melanosomes through interaction with SKIP
Title: Rab1A regulates anterograde melanosome transport by recruiting kinesin-1 to melanosomes through interaction with SKIP.
Results show that SNW1 directly associates with EFTUD2 and SNRNP200 and that disruption of SNW1 association with these proteins promotes the apoptosis of breast cancer cells.
Title: Inhibition of SNW1 association with spliceosomal proteins promotes apoptosis in breast cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D14S120 (e-PCR)
- UniSTS:15876

RH70062 (e-PCR)
- UniSTS:77841

D14S691E (e-PCR)
- UniSTS:90646

G35431 (e-PCR)
- UniSTS:27176

G36348 (e-PCR)
- UniSTS:74860

NoName (e-PCR)
- UniSTS:483951

SHGC-75044 (e-PCR)
- UniSTS:52618

G32556 (e-PCR)
- UniSTS:117140

SNW1_2342 (e-PCR)
- UniSTS:281024

D14S857 (e-PCR)
- UniSTS:16865

A009H42 (e-PCR)
- UniSTS:61937

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Notch binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA binding	HDA more info	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

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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)

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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_001318844.2 → NP_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:178 → 334

SKIP_SNW; SKIP/SNW domain
NM_012245.3 → NP_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:178 → 334

SKIP_SNW; SKIP/SNW domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

77717599..77761156 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

71926934..71971187 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

A8K8A9, Q13483, Q13573, Q32N03, Q5D0D6
XM_054375609.1 → XP_054231584.1 SNW domain-containing protein 1 isoform X1