Human Gene TSPAN2 (uc021osc.1) Description and Page Index
  Description: Homo sapiens tetraspanin 2 (TSPAN2), mRNA.
RefSeq Summary (NM_005725): The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015].
Transcript (Including UTRs)
   Position: hg19 chr1:115,590,633-115,632,121 Size: 41,489 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:115,593,111-115,632,053 Size: 38,943 Coding Exon Count: 7 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:115,590,633-115,632,121)mRNA (may differ from genome)Protein (193 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedStanford SOURCETreefam
UniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TSPAN2
CDC HuGE Published Literature: TSPAN2
Positive Disease Associations: Alcoholism , Body Composition , Body Height , Body Mass Index
Related Studies:
  1. Alcoholism
    Andrew C Heath et al. Biological psychiatry 2011, A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications., Biological psychiatry. [PubMed 21529783]
    We conclude that 1) meta-analyses of consumption data may contribute usefully to gene discovery; 2) translation of human alcoholism GWAS results to drug discovery or clinically useful prediction of risk will be challenging; and 3) through accumulation across studies, GWAS data may become valuable for improved genetic risk differentiation in research in biological psychiatry (e.g., prospective high-risk or resilience studies).
  2. Body Composition
    , , . [PubMed 0]
  3. Body Height
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TSPAN2
Diseases sorted by gene-association score: migraine with or without aura 1 (2)

-  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: 29.16 RPKM in Colon - Sigmoid
Total median expression: 234.24 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 -35.6068-0.524 Picture PostScript Text
3' UTR -597.452478-0.241 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
IPR023396 - CD81_extracellular
IPR000301 - Tetraspanin
IPR018499 - Tetraspanin/Peripherin
IPR018503 - Tetraspanin_CS
IPR008952 - Tetraspanin_EC2

Pfam Domains:
PF00335 - Tetraspanin family

SCOP Domains:
48652 - Tetraspanin

ModBase Predicted Comparative 3D Structure on D6PTH4
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC021675 - Homo sapiens tetraspanin 2, mRNA (cDNA clone MGC:22863 IMAGE:4042036), complete cds.
AF054839 - Homo sapiens tetraspan TM4SF (TSPAN-2) mRNA, complete cds.
GU971730 - Homo sapiens tetraspanin 2 isoform (TSPAN2) mRNA, complete cds, alternatively spliced.
AK315385 - Homo sapiens cDNA, FLJ96432, highly similar to Homo sapiens tetraspan 2 (TSPAN-2), mRNA.
KJ898156 - Synthetic construct Homo sapiens clone ccsbBroadEn_07550 TSPAN2 gene, encodes complete protein.
DQ893690 - Synthetic construct clone IMAGE:100006320; FLH195131.01X; RZPDo839E1283D tetraspanin 2 (TSPAN2) gene, encodes complete protein.
DQ893691 - Synthetic construct clone IMAGE:100006321; FLH195132.01X; RZPDo839F1283D tetraspanin 2 (TSPAN2) gene, encodes complete protein.
DQ893692 - Synthetic construct clone IMAGE:100006322; FLH195133.01X; RZPDo839G1283D tetraspanin 2 (TSPAN2) gene, encodes complete protein.
DQ893693 - Synthetic construct clone IMAGE:100006323; FLH195134.01X; RZPDo839H1283D tetraspanin 2 (TSPAN2) gene, encodes complete protein.
EU176787 - Synthetic construct Homo sapiens clone IMAGE:100011547; FLH195129.01L; RZPDo839C1283D tetraspanin 2 (TSPAN2) gene, encodes complete protein.
AK022144 - Homo sapiens cDNA FLJ12082 fis, clone HEMBB1002492.
JD538879 - Sequence 519903 from Patent EP1572962.
JD378481 - Sequence 359505 from Patent EP1572962.
JD299830 - Sequence 280854 from Patent EP1572962.
JD509760 - Sequence 490784 from Patent EP1572962.
JD509364 - Sequence 490388 from Patent EP1572962.
JD503906 - Sequence 484930 from Patent EP1572962.
JD409348 - Sequence 390372 from Patent EP1572962.
JD528452 - Sequence 509476 from Patent EP1572962.
JD348480 - Sequence 329504 from Patent EP1572962.
JD357100 - Sequence 338124 from Patent EP1572962.
JD559129 - Sequence 540153 from Patent EP1572962.
JD174592 - Sequence 155616 from Patent EP1572962.
JD265407 - Sequence 246431 from Patent EP1572962.
JD088002 - Sequence 69026 from Patent EP1572962.
JD510836 - Sequence 491860 from Patent EP1572962.
JD052990 - Sequence 34014 from Patent EP1572962.
JD239302 - Sequence 220326 from Patent EP1572962.
JD037261 - Sequence 18285 from Patent EP1572962.
JD502487 - Sequence 483511 from Patent EP1572962.
JD490642 - Sequence 471666 from Patent EP1572962.
JD466897 - Sequence 447921 from Patent EP1572962.
JD202014 - Sequence 183038 from Patent EP1572962.
JD555649 - Sequence 536673 from Patent EP1572962.
JD299464 - Sequence 280488 from Patent EP1572962.
JD434188 - Sequence 415212 from Patent EP1572962.
JD081836 - Sequence 62860 from Patent EP1572962.
JD516097 - Sequence 497121 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D6PTH4, D6PTH4_HUMAN, GU971730
UCSC ID: uc021osc.1
RefSeq Accession: NM_005725
Protein: D6PTH4

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: GU971730.1
exon count: 7CDS single in 3' UTR: no RNA size: 582
ORF size: 582CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1364.00frame 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.