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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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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

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