This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upr... See more...

Aliases for ITGA9 Gene

Aliases for ITGA9 Gene

  • Integrin Subunit Alpha 9 2 3 5
  • Integrin Alpha-RLC 3 4
  • Integrin Alpha-9 3 4
  • Integrin, Alpha 4-Like 2
  • Integrin, Alpha 9 2
  • ALPHA-RLC 3
  • ITGA4L 3
  • RLC 3

External Ids for ITGA9 Gene

Previous GeneCards Identifiers for ITGA9 Gene

  • GC03P036794
  • GC03P037306
  • GC03P037454

Summaries for ITGA9 Gene

Entrez Gene Summary for ITGA9 Gene

  • This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upregulated in small cell lung cancers. [provided by RefSeq, Jul 2008]

GeneCards Summary for ITGA9 Gene

ITGA9 (Integrin Subunit Alpha 9) is a Protein Coding gene. Diseases associated with ITGA9 include Chylothorax, Congenital and Arrhythmogenic Right Ventricular Cardiomyopathy. Among its related pathways are ERK Signaling and Sertoli-Sertoli Cell Junction Dynamics. Gene Ontology (GO) annotations related to this gene include collagen binding and laminin binding. An important paralog of this gene is ITGA4.

UniProtKB/Swiss-Prot Summary for ITGA9 Gene

  • Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin.

Gene Wiki entry for ITGA9 Gene

Additional gene information for ITGA9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ITGA9 Gene

Genomics for ITGA9 Gene

GeneHancer (GH) Regulatory Elements for ITGA9 Gene

Promoters and enhancers for ITGA9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J037451 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 515.5 +3.5 3485 8.4 HNRNPK CTCF NRF1 USF1 ZNF10 ZIC2 REST ZBTB10 ZBTB26 RAD21 ITGA9 LRRFIP2 GOLGA4 RF00951-105
GH03J037764 Enhancer 1.9 VISTA FANTOM5 Ensembl ENCODE CraniofacialAtlas 13.9 +317.4 317417 10.1 ZSCAN5C PHB2 ZNF639 ZBTB11 ZNF623 AFF1 TRIM28 TARDBP HES1 TOE1 ITGA9 RNU7-73P CTDSPL ITGA9-AS1 OXSR1 NDUFAF4P3 piR-48218-018
GH03J037476 Enhancer 1 FANTOM5 Ensembl ENCODE dbSUPER 22.7 +25.9 25863 3.6 ZNF146 ZNF384 RFX5 HNF4A GATA1 ESR1 ITGA9 RNU7-73P LRRFIP2 RF00951-105
GH03J037521 Enhancer 0.8 Ensembl ENCODE CraniofacialAtlas 21.2 +69.1 69140 1.5 NR2F2 RCOR1 CHD2 YY1 GATA2 POLR2A RAD21 ITGA9 RNU7-73P RF00951-105
GH03J037537 Enhancer 0.8 Ensembl ENCODE CraniofacialAtlas 17.6 +85.8 85840 2.5 MXI1 RCOR1 ATF2 CHD2 YY1 GATA2 RAD21 ITGA9 RNU7-73P RF00951-105
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ITGA9 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ITGA9

Top Transcription factor binding sites by QIAGEN in the ITGA9 gene promoter:
  • CREB
  • deltaCREB
  • FOXO4
  • HNF-1
  • HNF-1A
  • HTF
  • NRSF form 1
  • NRSF form 2
  • Zic3
  • ZID

Genomic Locations for ITGA9 Gene

Genomic Locations for ITGA9 Gene
chr3:37,452,115-37,823,507
(GRCh38/hg38)
Size:
371,393 bases
Orientation:
Plus strand
chr3:37,493,606-37,865,005
(GRCh37/hg19)
Size:
371,400 bases
Orientation:
Plus strand

Genomic View for ITGA9 Gene

Genes around ITGA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ITGA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ITGA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ITGA9 Gene

Proteins for ITGA9 Gene

  • Protein details for ITGA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13797-ITA9_HUMAN
    Recommended name:
    Integrin alpha-9
    Protein Accession:
    Q13797
    Secondary Accessions:
    • Q14638

    Protein attributes for ITGA9 Gene

    Size:
    1035 amino acids
    Molecular mass:
    114489 Da
    Quaternary structure:
    • Heterodimer of an alpha and a beta subunit. Alpha-9 (ITGA9) associates with beta-1 (ITGB1). Integrin ITGA9:ITGB1 interacts with FBLN5 (via N-terminus).

neXtProt entry for ITGA9 Gene

Post-translational modifications for ITGA9 Gene

  • Glycosylation at Asn225, Asn476, Asn493, Asn612, Asn654, Asn658, Asn672, Asn676, Asn807, Asn854, and Asn904
  • Modification sites at PhosphoSitePlus

Other Protein References for ITGA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ITGA9 Gene

Domains & Families for ITGA9 Gene

Gene Families for ITGA9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for ITGA9 Gene

Blocks:
  • Integrins alpha chain
  • Integrin alpha chain, C-terminal cytoplasmic region
  • FG-GAP
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ITGA9 Gene

GenScript: Design optimal peptide antigens:
  • Integrin alpha-RLC (ITA9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13797

UniProtKB/Swiss-Prot:

ITA9_HUMAN :
  • Belongs to the integrin alpha chain family.
Family:
  • Belongs to the integrin alpha chain family.
genes like me logo Genes that share domains with ITGA9: view

Function for ITGA9 Gene

Molecular function for ITGA9 Gene

UniProtKB/Swiss-Prot Function:
Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin.
UniProtKB/Swiss-Prot Induction:
Up-regulated in small cell lung cancers (SCLC).
GENATLAS Biochemistry:
integrin,alpha 9,cell surface adhesion receptor mediating cell-adhesion to extra cellular matrix or to other cells,through hetero dimerization and connecting to the cytoskeleton and various signaling molecules within cells,expressed in lung,small intestine and other cell lines,protein complexing with ITGB1

Phenotypes From GWAS Catalog for ITGA9 Gene

Gene Ontology (GO) - Molecular Function for ITGA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005518 collagen binding IEA --
GO:0043236 laminin binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ITGA9: view
genes like me logo Genes that share phenotypes with ITGA9: view

Animal Models for ITGA9 Gene

MGI Knock Outs for ITGA9:

Animal Model Products

  • Taconic Biosciences Mouse Models for ITGA9

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ITGA9

Clone Products

  • Addgene plasmids for ITGA9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ITGA9 Gene

Localization for ITGA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ITGA9 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ITGA9 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ITGA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0008305 integrin complex TAS 8245132
GO:0009925 basal plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ITGA9: view

Pathways & Interactions for ITGA9 Gene

PathCards logo

SuperPathways for ITGA9 Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
.66
.65
.64
.62
.57
2 Integrin Pathway
.67
.67
.56
.56
.38
3 Focal Adhesion
.33
4 MAPK-Erk Pathway
5 Actin Nucleation by ARP-WASP Complex
.66
.66
.41
.35
genes like me logo Genes that share pathways with ITGA9: view

Pathways by source for ITGA9 Gene

33 Qiagen pathways for ITGA9 Gene
  • Actin Nucleation and Branching
  • Actin Nucleation by ARP-WASP Complex
  • Actin-Based Motility by Rho Family GTPases
  • Akt Signaling
  • Calpain Protease Regulates Cellular Mechanics

Gene Ontology (GO) - Biological Process for ITGA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IGI 21060781
GO:0007229 integrin-mediated signaling pathway IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030593 neutrophil chemotaxis IEA --
GO:0042060 wound healing IEA --
genes like me logo Genes that share ontologies with ITGA9: view

No data available for SIGNOR curated interactions for ITGA9 Gene

Drugs & Compounds for ITGA9 Gene

(1) Drugs for ITGA9 Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
RGD (Arg-Gly-Asp) Peptides Pharma Inhibits integrin binding to RGD motifs 0

(1) ApexBio Compounds for ITGA9 Gene

Compound Action Cas Number
RGD (Arg-Gly-Asp) Peptides Inhibits integrin binding to RGD motifs 99896-85-2
genes like me logo Genes that share compounds with ITGA9: view

Drug Products

Transcripts for ITGA9 Gene

mRNA/cDNA for ITGA9 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ITGA9

Clone Products

  • Addgene plasmids for ITGA9

Alternative Splicing Database (ASD) splice patterns (SP) for ITGA9 Gene

No ASD Table

Relevant External Links for ITGA9 Gene

GeneLoc Exon Structure for
ITGA9

Expression for ITGA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ITGA9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ITGA9 Gene

This gene is overexpressed in Artery - Aorta (x4.1).

Protein differential expression in normal tissues from HIPED for ITGA9 Gene

This gene is overexpressed in Stomach (9.3), Heart (8.8), and Fetal gut (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ITGA9 Gene



Protein tissue co-expression partners for ITGA9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ITGA9

SOURCE GeneReport for Unigene cluster for ITGA9 Gene:

Hs.113157

mRNA Expression by UniProt/SwissProt for ITGA9 Gene:

Q13797-ITA9_HUMAN
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.

Evidence on tissue expression from TISSUES for ITGA9 Gene

  • Lung(4.4)
  • Intestine(4.3)
  • Liver(4.2)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with ITGA9: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ITGA9 Gene

Orthologs for ITGA9 Gene

This gene was present in the common ancestor of animals.

Orthologs for ITGA9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ITGA9 31 30
  • 99.48 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ITGA9 31 30
  • 91.01 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ITGA9 31 30
  • 90.18 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Itga9 17 31 30
  • 85.76 (n)
rat
(Rattus norvegicus)
Mammalia Itga9 30
  • 85.32 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ITGA9 31
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ITGA9 31
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves ITGA9 31 30
  • 77.27 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ITGA9 31
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia itga9 30
  • 71.3 (n)
zebrafish
(Danio rerio)
Actinopterygii itga9 31 30
  • 63.12 (n)
OneToOne
zgc63474 30
fruit fly
(Drosophila melanogaster)
Insecta alphaPS5 31 32
  • 22 (a)
ManyToMany
alphaPS4 31 32
  • 20 (a)
ManyToMany
scb 31 32
  • 20 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ina-1 32
  • 25 (a)
Species where no ortholog for ITGA9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ITGA9 Gene

ENSEMBL:
Gene Tree for ITGA9 (if available)
TreeFam:
Gene Tree for ITGA9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ITGA9: view image

Paralogs for ITGA9 Gene

(6) SIMAP similar genes for ITGA9 Gene using alignment to 4 proteins:

  • ITA9_HUMAN
  • E9PDS3_HUMAN
  • H7C2L1_HUMAN
  • L8E7C7_HUMAN
genes like me logo Genes that share paralogs with ITGA9: view

Variants for ITGA9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ITGA9 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
697425 Benign: not provided 37,506,010(+) G/A SYNONYMOUS_VARIANT
697426 Benign: not provided 37,542,595(+) C/T INTRON_VARIANT
697697 Benign: not provided 37,803,900(+) G/A SYNONYMOUS_VARIANT
701915 Benign: not provided 37,803,927(+) C/T SYNONYMOUS_VARIANT
702040 Benign: not provided 37,542,558(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ITGA9 Gene

Structural Variations from Database of Genomic Variants (DGV) for ITGA9 Gene

Variant ID Type Subtype PubMed ID
esv1009667 CNV insertion 20482838
esv1011375 CNV insertion 20482838
esv1186705 CNV insertion 17803354
esv1688032 CNV deletion 17803354
esv1931472 CNV deletion 18987734
esv23441 CNV loss 19812545
esv24143 CNV gain 19812545
esv2673591 CNV deletion 23128226
esv2725157 CNV deletion 23290073
esv2759140 CNV loss 17122850
esv28634 CNV gain 19812545
esv3307689 CNV mobile element insertion 20981092
esv3309034 CNV mobile element insertion 20981092
esv3336257 CNV insertion 20981092
esv3341274 CNV duplication 20981092
esv3357437 CNV insertion 20981092
esv3374754 CNV insertion 20981092
esv3568691 CNV loss 25503493
esv3595885 CNV gain 21293372
esv3595886 CNV gain 21293372
esv3595887 CNV gain 21293372
esv3595895 CNV gain 21293372
esv3595897 CNV loss 21293372
nsv1112822 CNV deletion 24896259
nsv1115639 CNV duplication 24896259
nsv1136716 CNV deletion 24896259
nsv1150057 CNV insertion 26484159
nsv1160928 CNV duplication 26073780
nsv3763 CNV insertion 18451855
nsv3764 CNV insertion 18451855
nsv3765 CNV deletion 18451855
nsv474798 CNV novel sequence insertion 20440878
nsv476421 CNV novel sequence insertion 20440878
nsv479701 CNV novel sequence insertion 20440878
nsv508910 CNV insertion 20534489
nsv518574 CNV gain 19592680
nsv522176 CNV loss 19592680
nsv527466 CNV loss 19592680
nsv834666 CNV gain+loss 17160897
nsv965158 CNV duplication 23825009
nsv979820 CNV duplication 23825009

Variation tolerance for ITGA9 Gene

Residual Variation Intolerance Score: 24.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.68; 57.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ITGA9 Gene

Human Gene Mutation Database (HGMD)
ITGA9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ITGA9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ITGA9 Gene

Disorders for ITGA9 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ITGA9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
chylothorax, congenital
  • hydrothorax, congenital
arrhythmogenic right ventricular cardiomyopathy
  • arrhythmogenic right ventricular dysplasia
lynch syndrome
  • colorectal cancer, hereditary nonpolyposis, type 1
- elite association - COSMIC cancer census association via MalaCards
Search ITGA9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ITGA9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ITGA9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ITGA9 Gene

Publications for ITGA9 Gene

  1. Sequence and tissue distribution of the integrin alpha 9 subunit, a novel partner of beta 1 that is widely distributed in epithelia and muscle. (PMID: 8245132) Palmer EL … Sheppard D (The Journal of cell biology 1993) 2 3 4 23 54
  2. Aberrant upregulation of a novel integrin alpha subunit gene at 3p21.3 in small cell lung cancer. (PMID: 8290272) Hibi K … Takahashi T (Oncogene 1994) 2 3 4 54
  3. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. (PMID: 22359512) Demirkan A … EUROSPAN consortium (PLoS genetics 2012) 3 41 54
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  5. Blood pressure and hypertension are associated with 7 loci in the Japanese population. (PMID: 20479155) Takeuchi F … Kato N (Circulation 2010) 3 41 54

Products for ITGA9 Gene

  • Signalway ELISA kits for ITGA9
  • Signalway Proteins for ITGA9

Sources for ITGA9 Gene