Human Gene ITGA9 (ENST00000264741.10_4) from GENCODE V47lift37
  Description: integrin subunit alpha 9 (from RefSeq NM_002207.3)
Gencode Transcript: ENST00000264741.10_4
Gencode Gene: ENSG00000144668.12_10
Transcript (Including UTRs)
   Position: hg19 chr3:37,493,632-37,864,998 Size: 371,367 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr3:37,493,866-37,860,480 Size: 366,615 Coding Exon Count: 28 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:37,493,632-37,864,998)mRNA (may differ from genome)Protein (1035 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ITA9_HUMAN
DESCRIPTION: RecName: Full=Integrin alpha-9; AltName: Full=Integrin alpha-RLC; Flags: Precursor;
FUNCTION: Integrin alpha-9/beta-1 is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G- I-E-L in cytotactin.
SUBUNIT: Heterodimer of an alpha and a beta subunit. Alpha-9 associates with beta-1.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: In airway epithelium, in the basal layer of squamous epithelium, and in smooth muscle, skeletal muscle, and hepatocytes. Abundantly expressed in fetal lung and lung cancers.
INDUCTION: Up-regulated in small cell lung cancers (SCLC).
SIMILARITY: Belongs to the integrin alpha chain family.
SIMILARITY: Contains 7 FG-GAP repeats.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ITGA9
Diseases sorted by gene-association score: chylothorax, congenital (11), muir-torre syndrome (5)

-  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: 15.70 RPKM in Thyroid
Total median expression: 214.87 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 -137.70234-0.588 Picture PostScript Text
3' UTR -1419.004518-0.314 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
IPR013517 - FG-GAP
IPR013519 - Int_alpha_beta-p
IPR000413 - Integrin_alpha
IPR013649 - Integrin_alpha-2
IPR018184 - Integrin_alpha_C_CS

Pfam Domains:
PF00357 - Integrin alpha cytoplasmic region
PF01839 - FG-GAP repeat
PF08441 - Integrin alpha
PF13517 - FG-GAP-like repeat

SCOP Domains:
69179 - Integrin domains
69318 - Integrin alpha N-terminal domain

ModBase Predicted Comparative 3D Structure on Q13797
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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 DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005518 collagen binding
GO:0043236 laminin binding
GO:0046872 metal ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0030198 extracellular matrix organization
GO:0030593 neutrophil chemotaxis
GO:0042060 wound healing

Cellular Component:
GO:0005886 plasma membrane
GO:0008305 integrin complex
GO:0009925 basal plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0034679 integrin alpha9-beta1 complex


-  Descriptions from all associated GenBank mRNAs
  D25303 - Homo sapiens mRNA for integrin alpha subunit, complete cds.
KJ901532 - Synthetic construct Homo sapiens clone ccsbBroadEn_10926 ITGA9 gene, encodes complete protein.
L24158 - Human integrin alpha 9 protein mRNA, 3'end.
BC030198 - Homo sapiens integrin, alpha 9, mRNA (cDNA clone MGC:34652 IMAGE:5199296), complete cds.
BX647350 - Homo sapiens mRNA; cDNA DKFZp779G058 (from clone DKFZp779G058).
JD022818 - Sequence 3842 from Patent EP1572962.
JD320121 - Sequence 301145 from Patent EP1572962.
JD546089 - Sequence 527113 from Patent EP1572962.
JD141700 - Sequence 122724 from Patent EP1572962.
JD335526 - Sequence 316550 from Patent EP1572962.
HW500560 - JP 2014045773-A/5: INHIBITORS OF MICRO-RNAs FOR USE FOR PREVENTING AND/OR ATTENUATING SKIN AGEING.
JC612223 - Sequence 5 from Patent EP2703498.
AK123884 - Homo sapiens cDNA FLJ41890 fis, clone OCBBF2024850.
AK026826 - Homo sapiens cDNA: FLJ23173 fis, clone LNG10019.

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

Protein Q13797 (Reactome details) participates in the following event(s):

R-HSA-216068 Interaction of integrin alpha9beta1 with Tenascin-C
R-HSA-265428 Interaction of integrin alpha9beta1 with VCAM1
R-HSA-374686 L1 interaction with Integrins
R-HSA-2681667 TNC binds Integrin alphaVbeta3, alphaVbeta6, alpha2beta1, alpha7beta1, alpha8beta1, alpha9beta1, alphaXbeta1
R-HSA-265424 SPP1 (osteopontin) binds integrin alpha5beta1, alpha9beta1
R-HSA-2467436 AGRN binds Integrins alphaVbeta1 (Other beta1-containing integrins)
R-HSA-216083 Integrin cell surface interactions
R-HSA-445144 Signal transduction by L1
R-HSA-3000178 ECM proteoglycans
R-HSA-1474244 Extracellular matrix organization
R-HSA-373760 L1CAM interactions
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000264741.1, ENST00000264741.2, ENST00000264741.3, ENST00000264741.4, ENST00000264741.5, ENST00000264741.6, ENST00000264741.7, ENST00000264741.8, ENST00000264741.9, ITA9_HUMAN, NM_002207, Q13797, Q14638, uc317hvg.1, uc317hvg.2
UCSC ID: ENST00000264741.10_4
RefSeq Accession: NM_002207.3
Protein: Q13797 (aka ITA9_HUMAN)

-  Gene Model Information
  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.