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Aliases for ISX Gene

Aliases for ISX Gene

  • Intestine Specific Homeobox 2 3 5
  • Intestine-Specific Homeobox 2 3
  • RAX-Like Homeobox 3 4
  • RAXLX 3 4
  • Pancreas-Intestine Homeodomain Transcription Factor 3
  • Pix-1 3

External Ids for ISX Gene

Previous GeneCards Identifiers for ISX Gene

  • GC22P033792
  • GC22P035462
  • GC22P018424

Summaries for ISX Gene

Entrez Gene Summary for ISX Gene

  • Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This gene is a member of the RAXLX homeobox gene family. [provided by RefSeq, Jul 2008]

GeneCards Summary for ISX Gene

ISX (Intestine Specific Homeobox) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is ARX.

UniProtKB/Swiss-Prot for ISX Gene

  • Transcription factor that regulates gene expression in intestine. May participate in vitamin A metabolism most likely by regulating BCO1 expression in the intestine (By similarity).

Additional gene information for ISX Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ISX Gene

Genomics for ISX Gene

GeneHancer (GH) Regulatory Elements for ISX Gene

Promoters and enhancers for ISX Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I035064 Promoter/Enhancer 1.3 EPDnew ENCODE 550.8 +0.7 685 4.7 HDAC1 ELF3 PKNOX1 FOXA2 BATF IRF4 RFX5 ATF7 IKZF2 RUNX3 ISX ISX-AS1 GC22P035086
GH22I035133 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 2 +68.8 68762 2.2 ZSCAN4 EBF1 ZIC2 TCF12 NCOR1 CBFA2T2 PRDM10 RUNX3 NRF1 CBFA2T3 LINC01399 ISX GC22P035126 ENSG00000238153
GH22I035024 Enhancer 0.7 ENCODE 0.3 -42.0 -41952 0.1 CTCF RB1 ZNF223 IRF3 ZNF2 IRF4 RAD21 SMC3 ZNF143 ZNF391 ISX-AS1 ISX
GH22I035047 Enhancer 0.4 FANTOM5 0.4 -18.7 -18661 0.2 RELA ISX-AS1 TOM1 HMOX1 ISX
GH22I035071 Enhancer 0.3 ENCODE 0.4 +5.9 5864 0.6 ZNF680 ISX-AS1 ISX GC22P035086
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ISX on UCSC Golden Path with GeneCards custom track

Genomic Locations for ISX Gene

Genomic Locations for ISX Gene
21,252 bases
Plus strand

Genomic View for ISX Gene

Genes around ISX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for ISX Gene

Proteins for ISX Gene

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

    Protein Symbol:
    Recommended name:
    Intestine-specific homeobox
    Protein Accession:
    Secondary Accessions:
    • Q68DJ5

    Protein attributes for ISX Gene

    245 amino acids
    Molecular mass:
    27011 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ISX Gene

Post-translational modifications for ISX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ISX Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ISX Gene

Domains & Families for ISX Gene

Gene Families for ISX Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ISX Gene

Suggested Antigen Peptide Sequences for ISX Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ISX: view

No data available for UniProtKB/Swiss-Prot for ISX Gene

Function for ISX Gene

Molecular function for ISX Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that regulates gene expression in intestine. May participate in vitamin A metabolism most likely by regulating BCO1 expression in the intestine (By similarity).

Phenotypes From GWAS Catalog for ISX Gene

Gene Ontology (GO) - Molecular Function for ISX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with ISX: view
genes like me logo Genes that share phenotypes with ISX: view

Animal Models for ISX Gene

MGI Knock Outs for ISX:

miRNA for ISX Gene

miRTarBase miRNAs that target ISX

Clone Products

  • Addgene plasmids for ISX

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

Localization for ISX Gene

Subcellular locations from UniProtKB/Swiss-Prot for ISX Gene


Subcellular locations from

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 ISX gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ISX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with ISX: view

Pathways & Interactions for ISX Gene

No Data Available

Gene Ontology (GO) - Biological Process for ISX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with ISX: view

No data available for Pathways by source and SIGNOR curated interactions for ISX Gene

Drugs & Compounds for ISX Gene

No Compound Related Data Available

Transcripts for ISX Gene

mRNA/cDNA for ISX Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ISX Gene

Intestine-specific homeobox:
Representative Sequences:

Clone Products

  • Addgene plasmids for ISX

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

No ASD Table

Relevant External Links for ISX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ISX Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Colon - Transverse (x33.8) and Small Intestine - Terminal Ileum (x16.7).

NURSA nuclear receptor signaling pathways regulating expression of ISX Gene:


SOURCE GeneReport for Unigene cluster for ISX Gene:


Evidence on tissue expression from TISSUES for ISX Gene

  • Intestine(2.5)
genes like me logo Genes that share expression patterns with ISX: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ISX Gene

Orthologs for ISX Gene

This gene was present in the common ancestor of animals.

Orthologs for ISX Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ISX 33 34
  • 99.05 (n)
(Canis familiaris)
Mammalia ISX 33 34
  • 79.89 (n)
(Bos Taurus)
Mammalia ISX 33 34
  • 78.27 (n)
(Rattus norvegicus)
Mammalia Isx 33
  • 72.54 (n)
(Mus musculus)
Mammalia Isx 33 16 34
  • 72.52 (n)
(Monodelphis domestica)
Mammalia ISX 34
  • 46 (a)
(Gallus gallus)
Aves ISX 33 34
  • 59.39 (n)
(Anolis carolinensis)
Reptilia ISX 34
  • 64 (a)
(Danio rerio)
Actinopterygii rx1 34
  • 22 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG11294 34
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
Species where no ortholog for ISX 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ISX Gene

Gene Tree for ISX (if available)
Gene Tree for ISX (if available)

Paralogs for ISX Gene

Paralogs for ISX Gene

(2) SIMAP similar genes for ISX Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with ISX: view

Variants for ISX Gene

Sequence variations from dbSNP and Humsavar for ISX Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000020131 -- 35,082,968(+) G/A intron_variant
rs1000240302 -- 35,086,906(+) T/C 3_prime_UTR_variant
rs1000507135 -- 35,076,993(+) C/T intron_variant
rs1000831719 -- 35,071,008(+) G/T intron_variant
rs1000967032 -- 35,071,218(+) T/G intron_variant

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

Variant ID Type Subtype PubMed ID
esv2661366 CNV deletion 23128226
esv26909 CNV gain 19812545
esv2758835 CNV loss 17122850
esv28292 CNV loss 19812545
esv34121 CNV loss 18971310
esv35003 CNV loss 17911159
esv3584500 CNV gain 24956385
esv3647659 CNV loss 21293372
nsv1118076 CNV deletion 24896259
nsv817989 CNV loss 17921354
nsv820628 CNV duplication 20802225
nsv834182 CNV gain 17160897
nsv834183 CNV gain 17160897

Variation tolerance for ISX Gene

Residual Variation Intolerance Score: 95.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.43; 77.24% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ISX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for ISX Gene

Additional Disease Information for ISX

No disorders were found for ISX Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ISX Gene

Publications for ISX Gene

  1. Intestine-Specific Homeobox Gene ISX Integrates IL6 Signaling, Tryptophan Catabolism, and Immune Suppression. (PMID: 28625979) Wang LT … Hsu SH (Cancer research 2017) 3 58
  2. Aryl hydrocarbon receptor promotes hepatocellular carcinoma tumorigenesis by targeting intestine-specific homeobox expression. (PMID: 28398627) Hsu SH … Wang SN (Molecular carcinogenesis 2017) 3 58
  3. Intestine-specific homeobox (ISX) induces intestinal metaplasia and cell proliferation to contribute to gastric carcinogenesis. (PMID: 26872890) Sue S … Maeda S (Journal of gastroenterology 2016) 3 58
  4. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PMID: 23314748) Nathan JA … Goldberg AL (The EMBO journal 2013) 3 58
  5. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX. (PMID: 23393141) Lobo GP … von Lintig J (The Journal of biological chemistry 2013) 3 58

Products for ISX Gene

  • Addgene plasmids for ISX

Sources for ISX Gene

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