Human Gene SKI (uc001aja.4) Description and Page Index
  Description: Homo sapiens v-ski sarcoma viral oncogene homolog (avian) (SKI), mRNA.
RefSeq Summary (NM_003036): This gene encodes the nuclear protooncogene protein homolog of avian sarcoma viral (v-ski) oncogene. It functions as a repressor of TGF-beta signaling, and may play a role in neural tube development and muscle differentiation. [provided by RefSeq, Oct 2009]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: X15218.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1966682, SAMEA1968189 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000378536.5/ ENSP00000367797.4 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:2,160,134-2,241,652 Size: 81,519 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr1:2,160,206-2,238,204 Size: 77,999 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:2,160,134-2,241,652)mRNA (may differ from genome)Protein (728 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SKI_HUMAN
DESCRIPTION: RecName: Full=Ski oncogene; AltName: Full=Proto-oncogene c-Ski;
FUNCTION: May play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. Functions as a repressor of TGF-beta signaling.
SUBUNIT: Interacts with SMAD2, SMAD3 and SMAD4. Interacts with HIPK2. Part of a complex with HIPK2 and SMAD1/2/3. Interacts with PRDM16 and SMAD3; the interaction with PRDM16 promotes the recruitment SMAD3-HDAC1 complex on the promoter of TGF-beta target genes.
INTERACTION: Q13485:SMAD4; NbExp=3; IntAct=EBI-347281, EBI-347263;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the SKI family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SKI
CDC HuGE Published Literature: SKI

-  MalaCards Disease Associations
  MalaCards Gene Search: SKI
Diseases sorted by gene-association score: shprintzen-goldberg syndrome* (1669), goldberg-shprintzen megacolon syndrome* (283), lung sarcoma (16), chromosome 1p36 deletion syndrome* (10), sarcoma (7), x-linked sideroblastic anemia with ataxia (7), anophthalmia/microphthalmia (5), craniosynostosis (4)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 93.81 RPKM in Brain - Cerebellum
Total median expression: 1267.82 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 -35.9072-0.499 Picture PostScript Text
3' UTR -1208.793448-0.351 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
IPR014890 - c-SKI_SMAD4-bd_dom
IPR009061 - DNA-bd_dom_put
IPR010919 - SAND_dom-like
IPR003380 - Transform_Ski
IPR023216 - Tscrpt_reg_SKI_SnoN

Pfam Domains:
PF02437 - SKI/SNO/DAC family
PF08782 - c-SKI Smad4 binding domain

SCOP Domains:
46955 - Putative DNA-binding domain
63763 - SAND domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1MR1
- X-ray MuPIT

1SBX
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P12755
FrontTopSide
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
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0019901 protein kinase binding
GO:0019904 protein domain specific binding
GO:0031625 ubiquitin protein ligase binding
GO:0046332 SMAD binding
GO:0046811 histone deacetylase inhibitor activity
GO:0070491 repressing transcription factor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001843 neural tube closure
GO:0002089 lens morphogenesis in camera-type eye
GO:0006351 transcription, DNA-templated
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0008283 cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0009948 anterior/posterior axis specification
GO:0010626 negative regulation of Schwann cell proliferation
GO:0014902 myotube differentiation
GO:0021772 olfactory bulb development
GO:0022011 myelination in peripheral nervous system
GO:0030177 positive regulation of Wnt signaling pathway
GO:0030326 embryonic limb morphogenesis
GO:0030509 BMP signaling pathway
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030514 negative regulation of BMP signaling pathway
GO:0031064 negative regulation of histone deacetylation
GO:0032926 negative regulation of activin receptor signaling pathway
GO:0035019 somatic stem cell population maintenance
GO:0043010 camera-type eye development
GO:0043388 positive regulation of DNA binding
GO:0043585 nose morphogenesis
GO:0045668 negative regulation of osteoblast differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048147 negative regulation of fibroblast proliferation
GO:0048593 camera-type eye morphogenesis
GO:0048666 neuron development
GO:0048741 skeletal muscle fiber development
GO:0048870 cell motility
GO:0060021 palate development
GO:0060041 retina development in camera-type eye
GO:0060325 face morphogenesis
GO:0060349 bone morphogenesis
GO:0060395 SMAD protein signal transduction
GO:0070207 protein homotrimerization

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0016604 nuclear body
GO:0016605 PML body
GO:0017053 transcriptional repressor complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  X15218 - Human ski oncogene mRNA.
BC156044 - Synthetic construct Homo sapiens clone IMAGE:100062305, MGC:190455 v-ski sarcoma viral oncogene homolog (avian) (SKI) mRNA, encodes complete protein.
BC157082 - Synthetic construct Homo sapiens clone IMAGE:100063408, MGC:190772 v-ski sarcoma viral oncogene homolog (avian) (SKI) mRNA, encodes complete protein.
JD371530 - Sequence 352554 from Patent EP1572962.
JD280872 - Sequence 261896 from Patent EP1572962.
AK309515 - Homo sapiens cDNA, FLJ99556.
JD040996 - Sequence 22020 from Patent EP1572962.
JD302220 - Sequence 283244 from Patent EP1572962.
JD476106 - Sequence 457130 from Patent EP1572962.
JD122159 - Sequence 103183 from Patent EP1572962.
JD422358 - Sequence 403382 from Patent EP1572962.
JD229509 - Sequence 210533 from Patent EP1572962.
JD098480 - Sequence 79504 from Patent EP1572962.
JD409534 - Sequence 390558 from Patent EP1572962.
JD365723 - Sequence 346747 from Patent EP1572962.
JD390212 - Sequence 371236 from Patent EP1572962.
JD122019 - Sequence 103043 from Patent EP1572962.
JD057256 - Sequence 38280 from Patent EP1572962.
JD393945 - Sequence 374969 from Patent EP1572962.
JD300934 - Sequence 281958 from Patent EP1572962.
JD404596 - Sequence 385620 from Patent EP1572962.
JD162459 - Sequence 143483 from Patent EP1572962.
JD548548 - Sequence 529572 from Patent EP1572962.
DQ569962 - Homo sapiens piRNA piR-30074, complete sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P12755 (Reactome details) participates in the following event(s):

R-HSA-201423 SKI complexes with the Smad complex, suppressing BMP2 signalling
R-HSA-173481 SKI/SKIL binds SMAD complex, suppressing TGF-beta signaling
R-NUL-2186736 Rnf111 binds SKI/SKIL in complex with SMAD2/3:SMAD4 upon TGF-beta stimulation
R-HSA-2186741 SMAD2/3 activation induces binding of RNF111/SMURF2 to SKI/SKIL
R-HSA-2186747 Ubiquitination of SKI/SKIL by RNF111/SMURF2
R-NUL-2186755 Ubiquitination of SKI/SKIL by Rnf111
R-HSA-201451 Signaling by BMP
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
R-HSA-162582 Signal Transduction
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003036, NP_003027, P12755, Q5SYT7, SKI_HUMAN
UCSC ID: uc001aja.4
RefSeq Accession: NM_003036
Protein: P12755 (aka SKI_HUMAN)
CCDS: CCDS39.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SKI:
sgs (Shprintzen-Goldberg Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003036.3
exon count: 7CDS single in 3' UTR: no RNA size: 5707
ORF size: 2187CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4299.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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