Human Gene SNW1 (ENST00000261531.12) from GENCODE V44
  Description: Homo sapiens SNW domain containing 1 (SNW1), transcript variant 2, mRNA. (from RefSeq NM_012245)
RefSeq Summary (NM_012245): 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].
Gencode Transcript: ENST00000261531.12
Gencode Gene: ENSG00000100603.14
Transcript (Including UTRs)
   Position: hg38 chr14:77,717,599-77,761,156 Size: 43,558 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr14:77,718,088-77,761,127 Size: 43,040 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr14:77,717,599-77,761,156)mRNA (may differ from genome)Protein (536 aa)
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OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=SNW domain-containing protein 1; AltName: Full=Nuclear protein SkiP; AltName: Full=Nuclear receptor coactivator NCoA-62; AltName: Full=Ski-interacting protein;
FUNCTION: Involved in vitamin D-mediated transcription. Can function as a splicing factor in pre-mRNA splicing.
SUBUNIT: Interacts with ATP1B4 (By similarity). Interacts with the SKI oncogene and with CHES1/FOXN3. Identified in the spliceosome C complex. Also associates with non-spliceosomal proteins.
INTERACTION: P43355:MAGEA1; NbExp=3; IntAct=EBI-632715, EBI-740978; P46531:NOTCH1; NbExp=3; IntAct=EBI-632715, EBI-636374; Q06330:RBPJ; NbExp=2; IntAct=EBI-632715, EBI-632552; Q96EB6:SIRT1; NbExp=7; IntAct=EBI-632715, EBI-1802965;
SIMILARITY: Belongs to the SNW family.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.67 RPKM in Testis
Total median expression: 1345.66 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.4029-0.255 Picture PostScript Text
3' UTR -126.80489-0.259 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017862 - SKI-int_prot_SKIP
IPR004015 - SKI-int_prot_SKIP_SNW-dom

Pfam Domains:
PF02731 - SKIP/SNW domain

ModBase Predicted Comparative 3D Structure on Q13573
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
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Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0005112 Notch binding
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0035257 nuclear hormone receptor binding
GO:0042809 vitamin D receptor binding
GO:0042974 retinoic acid receptor binding
GO:0046332 SMAD binding
GO:0050681 androgen receptor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000350 generation of catalytic spliceosome for second transesterification step
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0007219 Notch signaling pathway
GO:0007221 positive regulation of transcription of Notch receptor target
GO:0008380 RNA splicing
GO:0016032 viral process
GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway
GO:0042771 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0043923 positive regulation by host of viral transcription
GO:0045747 positive regulation of Notch signaling pathway
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048026 positive regulation of mRNA splicing, via spliceosome
GO:0048384 retinoic acid receptor signaling pathway
GO:0048385 regulation of retinoic acid receptor signaling pathway
GO:0050769 positive regulation of neurogenesis
GO:0051571 positive regulation of histone H3-K4 methylation
GO:0070562 regulation of vitamin D receptor signaling pathway
GO:0070564 positive regulation of vitamin D receptor signaling pathway
GO:0071300 cellular response to retinoic acid

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0016363 nuclear matrix
GO:0016604 nuclear body
GO:0016607 nuclear speck
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:0071014 post-mRNA release spliceosomal complex
GO:0008024 cyclin/CDK positive transcription elongation factor complex

-  Descriptions from all associated GenBank mRNAs
  BC051806 - Homo sapiens cDNA clone IMAGE:5755350, partial cds.
BC040112 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone IMAGE:5581513), partial cds.
BC046105 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone IMAGE:5123391), partial cds.
AX775981 - Sequence 251 from Patent WO03048202.
U51432 - Homo sapiens nuclear protein Skip mRNA, complete cds.
AF045184 - Homo sapiens nuclear receptor coactivator NCoA-62 mRNA, complete cds.
AK292274 - Homo sapiens cDNA FLJ76433 complete cds, highly similar to Homo sapiens SNW domain containing 1 (SNW1), mRNA.
AK302246 - Homo sapiens cDNA FLJ51388 complete cds, highly similar to SNW domain-containing protein 1.
AK316087 - Homo sapiens cDNA, FLJ78986 complete cds, highly similar to SNW domain-containing protein 1.
BC108903 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone MGC:119379 IMAGE:40006529), complete cds.
AK293619 - Homo sapiens cDNA FLJ59238 complete cds, highly similar to SNW domain-containing protein 1.
BT020060 - Homo sapiens SKI-interacting protein mRNA, complete cds.
BT020061 - Homo sapiens SKI-interacting protein mRNA, complete cds.
KJ898426 - Synthetic construct Homo sapiens clone ccsbBroadEn_07820 SNW1 gene, encodes complete protein.
AB464230 - Synthetic construct DNA, clone: pF1KB7823, Homo sapiens SNW1 gene for SNW domain containing 1, without stop codon, in Flexi system.
CR457433 - Homo sapiens full open reading frame cDNA clone RZPDo834B066D for gene SNW1, SKI-interacting protein; complete cds, incl. stopcodon.
JD370948 - Sequence 351972 from Patent EP1572962.
BC108902 - Homo sapiens cDNA clone IMAGE:40006528.
JD177740 - Sequence 158764 from Patent EP1572962.
BC032377 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone IMAGE:5111389).
BC065286 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone IMAGE:6015770), partial cds.
BC105585 - Homo sapiens SNW domain containing 1, mRNA (cDNA clone IMAGE:6738734), partial cds.
LF209618 - JP 2014500723-A/17121: Polycomb-Associated Non-Coding RNAs.
MA445195 - JP 2018138019-A/17121: Polycomb-Associated Non-Coding RNAs.
JD151878 - Sequence 132902 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome
hsa04330 - Notch signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q13573 (Reactome details) participates in the following event(s):

R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-5252001 ATP1B4 binds SNW1
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-1912394 NICD1 in complex with RBPJ (CSL) recruits MAML
R-HSA-1912388 NICD1 displaces co-repressor complex from RBPJ (CSL)
R-NUL-2064264 NICD1 displaces NCOR co-repressor complex from CSL
R-HSA-1912391 NICD1 is phosphorylated by CDK8
R-NUL-2065178 CDK8 phosphorylates xNICD1
R-HSA-2220971 CDK8 phosphorylates NICD1 PEST domain mutants
R-NUL-4396363 mNICD1 Chimeric Enhancer Complex binds Hes1 promoter
R-HSA-2220964 NICD1 PEST domain mutants in complex with RBPJ (CSL) bind MAML
R-HSA-2220982 NICD1 PEST domain mutants displace co-repressor complex from RBPJ (CSL)
R-HSA-212356 Formation of CSL-NICD coactivator complex
R-HSA-1912393 MAML in complex with NICD1 recruits CDK8
R-HSA-4396347 NOTCH1 Coactivator Complex binds HES1 promoter
R-HSA-4396371 NOTCH1 Coactivator Complex binds MYC promoter
R-HSA-4396379 NOTCH1 Coactivator Complex binds HES5 promoter
R-HSA-4396382 NOTCH1 Coactivator Complex binds promoters of HEY genes
R-HSA-8878220 RUNX3 binds the NOTCH1 coactivator complex
R-HSA-9017835 NOTCH1 coactivator complex binds NOTCH3 gene
R-NUL-2064916 MAML recruits CDK8:CCNC to xNICD1
R-HSA-2220957 NOTCH1 PEST domain mutants coactivator complex binds CDK8:CCNC
R-HSA-4396392 NOTCH1 PEST domain mutants bind HES1 promoter
R-HSA-4396393 NOTCH1 PEST domain mutants bind MYC promoter
R-HSA-4396401 NOTCH1 PEST domain mutants bind HES5 promoter
R-HSA-4396402 NOTCH1 PEST domain mutants bind promoters of HEY genes
R-HSA-8878237 RUNX3:NOTCH1 coactivator complex binds the HES1 gene promoter
R-HSA-9021451 NOTCH1,NOTCH3 coactivator complex binds PLXND1 gene promoter
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-157052 NICD traffics to nucleus
R-HSA-350054 Notch-HLH transcription pathway
R-HSA-72172 mRNA Splicing
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
R-HSA-8941856 RUNX3 regulates NOTCH signaling
R-HSA-1912408 Pre-NOTCH Transcription and Translation
R-HSA-1980143 Signaling by NOTCH1
R-HSA-2644602 Signaling by NOTCH1 PEST Domain Mutants in Cancer
R-HSA-2894858 Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer
R-HSA-212436 Generic Transcription Pathway
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-9013508 NOTCH3 Intracellular Domain Regulates Transcription
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-1912422 Pre-NOTCH Expression and Processing
R-HSA-157118 Signaling by NOTCH
R-HSA-2644603 Signaling by NOTCH1 in Cancer
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-8953854 Metabolism of RNA
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-9012852 Signaling by NOTCH3
R-HSA-162582 Signal Transduction
R-HSA-5663202 Diseases of signal transduction
R-HSA-74160 Gene expression (Transcription)
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8A9, ENST00000261531.1, ENST00000261531.10, ENST00000261531.11, ENST00000261531.2, ENST00000261531.3, ENST00000261531.4, ENST00000261531.5, ENST00000261531.6, ENST00000261531.7, ENST00000261531.8, ENST00000261531.9, NM_012245, Q13483, Q13573, Q32N03, Q5D0D6, SKIIP, SKIP, SNW1_HUMAN, uc001xuf.1, uc001xuf.2, uc001xuf.3, uc001xuf.4, uc001xuf.5
UCSC ID: ENST00000261531.12
RefSeq Accession: NM_012245
Protein: Q13573 (aka SNW1_HUMAN)
CCDS: CCDS9867.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.