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    IRX2-DT IRX2 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 153571, updated on 5-Mar-2024

    Summary

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    Official Symbol
    IRX2-DTprovided by HGNC
    Official Full Name
    IRX2 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:24226
    See related
    MIM:610522; AllianceGenome:HGNC:24226
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CEI; IRX2NB; C5orf38
    Summary
    Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in lung (RPKM 1.7), fat (RPKM 0.8) and 9 other tissues See more
    Orthologs
    all
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    Genomic context

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    See IRX2-DT in Genome Data Viewer
    Location:
    5p15.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (2751893..2758578)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (2666906..2673593)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (2752007..2758692)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long stress-induced non-coding transcript 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2747930-2748875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2748876-2749820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2751906-2752830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2756718-2757670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2757671-2758621 Neighboring gene iroquois homeobox 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:2760035-2760224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2780330-2781266 Neighboring gene 3-hydroxyisobutyryl-Coenzyme A hydrolase pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:2850224-2851423 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2862446-2863184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:2863185-2863922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2863923-2864660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:2864661-2865398 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:2914965-2915913 Neighboring gene uncharacterized LOC105374620

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. [High-resolution analysis of chromosome 5 and identification of candidate genes in gastric cancer]. Yu YY, et al. Zhonghua Zhong Liu Za Zhi, 2006 Feb. PMID 16750006
    2. A novel primate specific gene, CEI, is located in the homeobox gene IRXA2 promoter in Homo sapiens. Wu Q, et al. Gene, 2006 Apr 26. PMID 16515847
    3. Genome-wide association study of selenium concentrations. Cornelis MC, et al. Hum Mol Genet, 2015 Mar 1. PMID 25343990, Free PMC Article
    4. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Brandenberger R, et al. Nat Biotechnol, 2004 Jun. PMID 15146197
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CEI may play an important role in the evolution of higher primates in coordination with the IRX genes
      Title: A novel primate specific gene, CEI, is located in the homeobox gene IRXA2 promoter in Homo sapiens.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of selenium concentrations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Other Names

    • IRX2 neighbor
    • coordinated expression to IRX2
    • coordinated expression to IRXA2 homeobox
    • coordinated expression to IRXA2 protein

    Clone Names

    • MGC126657, MGC126683

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    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.

    RNA

    1. NR_122125.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translation start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC091891, AY249325, BC143640, BX090247

    2. NR_122126.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translation start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC091891, AY249325, BC143638, BX090247

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      2751893..2758578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      2666906..2673593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001294337.2: Suppressed sequence

      Description
      NM_001294337.2: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    2. NM_001306149.2: Suppressed sequence

      Description
      NM_001306149.2: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    3. NM_001306150.2: Suppressed sequence

      Description
      NM_001306150.2: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    4. NM_001365685.1: Suppressed sequence

      Description
      NM_001365685.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    5. NM_001365688.1: Suppressed sequence

      Description
      NM_001365688.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    6. NM_001365689.1: Suppressed sequence

      Description
      NM_001365689.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    7. NM_178569.4: Suppressed sequence

      Description
      NM_178569.4: This RefSeq was removed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86SI9.1 GenPept UniProtKB/Swiss-Prot:Q86SI9

    Gene LinkOut

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

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