Human Gene TUSC1 (uc003zpx.3) Description and Page Index
  Description: Homo sapiens tumor suppressor candidate 1 (TUSC1), mRNA.
RefSeq Summary (NM_001004125): This gene is located within the region of chromosome 9p that harbors tumor suppressor genes critical in carcinogenesis. It is an intronless gene which is downregulated in non-small-cell lung cancer and small-cell lung cancer cell lines, suggesting that it may play a role in lung tumorigenesis. [provided by RefSeq, Jul 2008]. 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. ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr9:25,676,387-25,678,856 Size: 2,470 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr9:25,677,681-25,678,319 Size: 639 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:25,676,387-25,678,856)mRNA (may differ from genome)Protein (212 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TUSC1_HUMAN
DESCRIPTION: RecName: Full=Tumor suppressor candidate gene 1 protein; AltName: Full=TSG-9; Short=TSG9;
TISSUE SPECIFICITY: Widely expressed at low level. Expressed at higher level in testis, weakly expressed in muscle, colon, lung and spleen. Not detected in 3 non small cell lung carcinoma (NSCLC) cell lines with homozygous deletion of the 9p region, while it is down-regulated in 3 other tumor cell lines.
CAUTION: It is uncertain whether Met-1 or Met-4 is the initiator.
SEQUENCE CAUTION: Sequence=AAO38227.2; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TUSC1
CDC HuGE Published Literature: TUSC1
Positive Disease Associations: Aorta , Carotid Artery Diseases , Cholesterol , Drug-Induced Liver Injury , E-Selectin , Gallbladder Neoplasms , Hematocrit , Hemoglobins , Hypertension , Prostatic Neoplasms , Schizophrenia , Smoking , Socioeconomic Factors , Triglycerides
Related Studies:
  1. Aorta
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
  2. Carotid Artery Diseases
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
  3. Carotid Artery Diseases
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 20.89 RPKM in Testis
Total median expression: 400.95 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -229.91537-0.428 Picture PostScript Text
3' UTR -341.591294-0.264 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
  ModBase Predicted Comparative 3D Structure on Q2TAM9
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AY168647 - Homo sapiens TUSC1 mRNA, complete cds.
BC036931 - Homo sapiens tumor suppressor candidate 1, mRNA (cDNA clone IMAGE:5244091).
BC028316 - Homo sapiens tumor suppressor candidate 1, mRNA (cDNA clone IMAGE:5190302), partial cds.
BC046919 - Homo sapiens tumor suppressor candidate 1, mRNA (cDNA clone IMAGE:5466772), partial cds.
BC110824 - Homo sapiens tumor suppressor candidate 1, mRNA (cDNA clone MGC:131751 IMAGE:5169320), complete cds.
BC017510 - Homo sapiens tumor suppressor candidate 1, mRNA (cDNA clone IMAGE:4860718), partial cds.
JD368479 - Sequence 349503 from Patent EP1572962.
JD390930 - Sequence 371954 from Patent EP1572962.
JD109519 - Sequence 90543 from Patent EP1572962.
JD394523 - Sequence 375547 from Patent EP1572962.
JD086254 - Sequence 67278 from Patent EP1572962.
JD455971 - Sequence 436995 from Patent EP1572962.
JD192528 - Sequence 173552 from Patent EP1572962.
JD418547 - Sequence 399571 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0PJ78, NM_001004125, NP_001004125, Q2TAM9, Q67GI3, Q86SS1, Q8TAH8, TUSC1_HUMAN
UCSC ID: uc003zpx.3
RefSeq Accession: NM_001004125
Protein: Q2TAM9 (aka TUSC1_HUMAN)
CCDS: CCDS34999.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001004125.2
exon count: 1CDS single in 3' UTR: no RNA size: 2477
ORF size: 639CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1367.00frame shift in genome: no % Coverage: 99.72
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.