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    Isx intestine specific homeobox [ Mus musculus (house mouse) ]

    Gene ID: 71597, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Isxprovided by MGI
    Official Full Name
    intestine specific homeoboxprovided by MGI
    Primary source
    MGI:MGI:1918847
    See related
    Ensembl:ENSMUSG00000031621 AllianceGenome:MGI:1918847
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Pix-1; 9130012O13Rik
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Acts upstream of or within negative regulation of intestinal absorption; regulation of transcription by RNA polymerase II; and regulation of vitamin A metabolic process. Predicted to be located in nucleus. Is expressed in genitourinary system; midgut; and thymus. Orthologous to human ISX (intestine specific homeobox). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in large intestine adult (RPKM 83.9), duodenum adult (RPKM 41.5) and 2 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    8 C1; 8 35.54 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (75599326..75620134)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (74873174..74893506)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_21897 Neighboring gene STARR-seq mESC enhancer starr_21898 Neighboring gene STARR-seq mESC enhancer starr_21899 Neighboring gene STARR-seq mESC enhancer starr_21900 Neighboring gene complement receptor related protein, pseudogene Neighboring gene STARR-seq mESC enhancer starr_21901 Neighboring gene STARR-seq mESC enhancer starr_21902 Neighboring gene STARR-seq mESC enhancer starr_21903 Neighboring gene Luc7 homolog-like pseudogene Neighboring gene STARR-seq mESC enhancer starr_21904 Neighboring gene STARR-seq mESC enhancer starr_21905 Neighboring gene STARR-seq mESC enhancer starr_21906 Neighboring gene STARR-seq mESC enhancer starr_21907 Neighboring gene STARR-seq mESC enhancer starr_21908 Neighboring gene STARR-seq mESC enhancer starr_21909 Neighboring gene STARR-seq mESC enhancer starr_21910 Neighboring gene STARR-seq mESC enhancer starr_21911 Neighboring gene STARR-seq mESC enhancer starr_21912 Neighboring gene STARR-seq mESC enhancer starr_21913 Neighboring gene STARR-seq mESC enhancer starr_21915 Neighboring gene STARR-seq mESC enhancer starr_21916 Neighboring gene STARR-seq mESC enhancer starr_21917 Neighboring gene STARR-positive B cell enhancer ABC_E6664 Neighboring gene STARR-seq mESC enhancer starr_21922 Neighboring gene STARR-seq mESC enhancer starr_21923 Neighboring gene predicted gene, 53440 Neighboring gene HMG box domain containing 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Transcription factor ISX mediates the cross talk between diet and immunity. Widjaja-Adhi MAK, et al. Proc Natl Acad Sci U S A, 2017 Oct 24. PMID 29073082, Free PMC Article
    2. Protective role of carotenoids in the visual cycle. Widjaja-Adhi MAK, et al. FASEB J, 2018 Jun 8. PMID 29882710, Free PMC Article
    3. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX. Lobo GP, et al. J Biol Chem, 2013 Mar 29. PMID 23393141, Free PMC Article
    4. Isx participates in the maintenance of vitamin A metabolism by regulation of beta-carotene 15,15'-monooxygenase (Bcmo1) expression. Seino Y, et al. J Biol Chem, 2008 Feb 22. PMID 18093975
    5. A genetic dissection of intestinal fat-soluble vitamin and carotenoid absorption. Widjaja-Adhi MA, et al. Hum Mol Genet, 2015 Jun 1. PMID 25701869, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX
      Title: Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX.
    2. Isx participates in the maintenance of vitamin A metabolism by regulating Bcmo1 expression in the intestine.
      Title: Isx participates in the maintenance of vitamin A metabolism by regulation of beta-carotene 15,15'-monooxygenase (Bcmo1) expression.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2)  1 citation
    • Endonuclease-mediated (2) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of intestinal absorption IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of vitamin A metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    intestine-specific homeobox
    Names
    pancreas-intestine homeodomain transcription factor

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001294278.2 → NP_001281207.1  intestine-specific homeobox isoform 1

      See identical proteins and their annotated locations for NP_001281207.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL603782
      Consensus CDS
      CCDS80899.1
      UniProtKB/Swiss-Prot
      A1A546
      Related
      ENSMUSP00000134368.2, ENSMUST00000174427.2
      Conserved Domains (1) summary
      pfam00046
      Location:82 → 134
      Homeobox; Homeobox domain

    2. NM_027837.4 → NP_082113.2  intestine-specific homeobox isoform 2

      See identical proteins and their annotated locations for NP_082113.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of an exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL603782
      Consensus CDS
      CCDS40391.1
      UniProtKB/Swiss-Prot
      A1A545, A1A546, Q9D2Z0
      UniProtKB/TrEMBL
      B1Q2M1
      Related
      ENSMUSP00000034034.3, ENSMUST00000034034.10
      Conserved Domains (1) summary
      pfam00046
      Location:82 → 134
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000074.7 Reference GRCm39 C57BL/6J

      Range
      75599326..75620134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1A546.2 GenPept UniProtKB/Swiss-Prot:A1A546

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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