Human Gene TSPAN9 (uc001qlp.3) Description and Page Index
  Description: Homo sapiens tetraspanin 9 (TSPAN9), transcript variant 1, mRNA.
RefSeq Summary (NM_006675): 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. Alternatively spliced transcripts encoding the same protein have been identified. [provided by RefSeq, Nov 2009].
Transcript (Including UTRs)
   Position: hg19 chr12:3,186,521-3,395,730 Size: 209,210 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr12:3,310,360-3,392,282 Size: 81,923 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:3,186,521-3,395,730)mRNA (may differ from genome)Protein (239 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TSN9_HUMAN
DESCRIPTION: RecName: Full=Tetraspanin-9; Short=Tspan-9; AltName: Full=Tetraspan NET-5;
SUBUNIT: Found in a complex with GP6 (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (By similarity). Note=Colocalizes with GP6 in tetraspanin microdomains on the platelet surface (By similarity).
TISSUE SPECIFICITY: Expressed in megakaryocytes and platelets (at protein level).
PTM: Glycosylated (By similarity).
SIMILARITY: Belongs to the tetraspanin (TM4SF) family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TSPAN9
CDC HuGE Published Literature: TSPAN9

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 86.83 RPKM in Brain - Cerebellum
Total median expression: 752.48 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 -76.20183-0.416 Picture PostScript Text
3' UTR -1520.703448-0.441 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
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 O75954
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     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0007166 cell surface receptor signaling pathway
GO:0008150 biological_process

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0097197 tetraspanin-enriched microdomain


-  Descriptions from all associated GenBank mRNAs
  AK223179 - Homo sapiens mRNA for tetraspan NET-5 variant, clone: PNC04977.
AK027366 - Homo sapiens cDNA FLJ14460 fis, clone HEMBB1002600, highly similar to Tetraspanin-9.
AF089749 - Homo sapiens tetraspan NET-5 mRNA, complete cds.
BC071881 - Homo sapiens tetraspanin 9, mRNA (cDNA clone MGC:88555 IMAGE:6256950), complete cds.
JD236192 - Sequence 217216 from Patent EP1572962.
JD081104 - Sequence 62128 from Patent EP1572962.
JD268803 - Sequence 249827 from Patent EP1572962.
JD052860 - Sequence 33884 from Patent EP1572962.
CR542109 - Homo sapiens full open reading frame cDNA clone RZPDo834H0637D for gene NET-5, transmembrane 4 superfamily member tetraspan NET-5; complete cds, incl. stopcodon.
JD099346 - Sequence 80370 from Patent EP1572962.
JD289931 - Sequence 270955 from Patent EP1572962.
JD524911 - Sequence 505935 from Patent EP1572962.
JD515935 - Sequence 496959 from Patent EP1572962.
JD376207 - Sequence 357231 from Patent EP1572962.
JD496780 - Sequence 477804 from Patent EP1572962.
JD180977 - Sequence 162001 from Patent EP1572962.
JD376950 - Sequence 357974 from Patent EP1572962.
JD538406 - Sequence 519430 from Patent EP1572962.
JD480333 - Sequence 461357 from Patent EP1572962.
JD367472 - Sequence 348496 from Patent EP1572962.
JD059511 - Sequence 40535 from Patent EP1572962.
JD290751 - Sequence 271775 from Patent EP1572962.
JD327758 - Sequence 308782 from Patent EP1572962.
AY523992 - Homo sapiens cardiac-specific heart failure-associated protein (HSFA) mRNA, complete cds; alternatively spliced.
JD176948 - Sequence 157972 from Patent EP1572962.
JD400538 - Sequence 381562 from Patent EP1572962.
LF383546 - JP 2014500723-A/191049: Polycomb-Associated Non-Coding RNAs.
LF207414 - JP 2014500723-A/14917: Polycomb-Associated Non-Coding RNAs.
LF366045 - JP 2014500723-A/173548: Polycomb-Associated Non-Coding RNAs.
LF366044 - JP 2014500723-A/173547: Polycomb-Associated Non-Coding RNAs.
LF366043 - JP 2014500723-A/173546: Polycomb-Associated Non-Coding RNAs.
JD473471 - Sequence 454495 from Patent EP1572962.
AF217967 - Homo sapiens clone PP1057 unknown mRNA.
JD466409 - Sequence 447433 from Patent EP1572962.
JD425570 - Sequence 406594 from Patent EP1572962.
JD475773 - Sequence 456797 from Patent EP1572962.
JD180905 - Sequence 161929 from Patent EP1572962.
JD179472 - Sequence 160496 from Patent EP1572962.
JD037447 - Sequence 18471 from Patent EP1572962.
JD223152 - Sequence 204176 from Patent EP1572962.
JD544050 - Sequence 525074 from Patent EP1572962.
JD374093 - Sequence 355117 from Patent EP1572962.
JD289999 - Sequence 271023 from Patent EP1572962.
BC034280 - Homo sapiens tetraspanin 9, mRNA (cDNA clone IMAGE:4779587).
JD260500 - Sequence 241524 from Patent EP1572962.
JD258268 - Sequence 239292 from Patent EP1572962.
JD231593 - Sequence 212617 from Patent EP1572962.
JD163048 - Sequence 144072 from Patent EP1572962.
JD140764 - Sequence 121788 from Patent EP1572962.
JD156060 - Sequence 137084 from Patent EP1572962.
JD106271 - Sequence 87295 from Patent EP1572962.
JD376197 - Sequence 357221 from Patent EP1572962.
JD221738 - Sequence 202762 from Patent EP1572962.
JD418464 - Sequence 399488 from Patent EP1572962.
JD283774 - Sequence 264798 from Patent EP1572962.
JD514565 - Sequence 495589 from Patent EP1572962.
JD418887 - Sequence 399911 from Patent EP1572962.
JD177251 - Sequence 158275 from Patent EP1572962.
JD375475 - Sequence 356499 from Patent EP1572962.
JD341336 - Sequence 322360 from Patent EP1572962.
JD341337 - Sequence 322361 from Patent EP1572962.
JD091640 - Sequence 72664 from Patent EP1572962.
JD104826 - Sequence 85850 from Patent EP1572962.
JD270629 - Sequence 251653 from Patent EP1572962.
JD477452 - Sequence 458476 from Patent EP1572962.
JD218644 - Sequence 199668 from Patent EP1572962.
JD270749 - Sequence 251773 from Patent EP1572962.
JD536352 - Sequence 517376 from Patent EP1572962.
JD427040 - Sequence 408064 from Patent EP1572962.
MA619123 - JP 2018138019-A/191049: Polycomb-Associated Non-Coding RNAs.
MA601622 - JP 2018138019-A/173548: Polycomb-Associated Non-Coding RNAs.
MA601621 - JP 2018138019-A/173547: Polycomb-Associated Non-Coding RNAs.
MA601620 - JP 2018138019-A/173546: Polycomb-Associated Non-Coding RNAs.
MA442991 - JP 2018138019-A/14917: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DUQ7, NET5, NM_006675, NP_006666, O75954, Q53FV2, Q6FGJ8, TSN9_HUMAN
UCSC ID: uc001qlp.3
RefSeq Accession: NM_006675
Protein: O75954 (aka TSN9_HUMAN)
CCDS: CCDS8520.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006675.4
exon count: 9CDS single in 3' UTR: no RNA size: 4351
ORF size: 720CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1568.00frame 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.