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    HDX highly divergent homeobox [ Homo sapiens (human) ]

    Gene ID: 139324, updated on 27-Aug-2024

    Summary

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    Official Symbol
    HDXprovided by HGNC
    Official Full Name
    highly divergent homeoboxprovided by HGNC
    Primary source
    HGNC:HGNC:26411
    See related
    Ensembl:ENSG00000165259 MIM:300994; AllianceGenome:HGNC:26411
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CXorf43; D030011N01Rik
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    Xq21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (84317878..84502453, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (82754225..82938810, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (83572886..83757461, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S6 kinase A6 Neighboring gene microRNA 548i-4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:83643706-83644905 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20911 Neighboring gene NANOG hESC enhancer GRCh37_chrX:83968054-83968555 Neighboring gene testis expressed 16, pseudogene Neighboring gene SET pseudogene 4 Neighboring gene ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)

    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 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. Promoter-associated proteins of EPAS1 identified by enChIP-MS - A putative role of HDX as a negative regulator. Hamidian A, et al. Biochem Biophys Res Commun, 2018 May 5. PMID 29577908
    2. 14-3-3 epsilon dynamically interacts with key components of mitogen-activated protein kinase signal module for selective modulation of the TNF-alpha-induced time course-dependent NF-kappaB activity. Zuo S, et al. J Proteome Res, 2010 Jul 2. PMID 20462248
    3. A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Jirawatnotai S, et al. Nature, 2011 Jun 8. PMID 21654808, Free PMC Article
    4. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. Oliviero G, et al. Sci Rep, 2015 Dec 21. PMID 26687479, Free PMC Article
    5. Identification of proximal SUMO-dependent interactors using SUMO-ID. Barroso-Gomila O, et al. Nat Commun, 2021 Nov 18. PMID 34795231, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HDX negatively regulates EPAS1 expression through a release-of-inhibition mechanism.
      Title: Promoter-associated proteins of EPAS1 identified by enChIP-MS - A putative role of HDX as a negative regulator.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30678, MGC126769, MGC126771

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    highly divergent homeobox

    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.

    Genomic

    1. NG_017158.2 RefSeqGene

      Range
      5027..189602
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177478.2 → NP_001170949.1  highly divergent homeobox isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK055240, AL035552
      Consensus CDS
      CCDS55456.1
      UniProtKB/Swiss-Prot
      Q7Z353
      Related
      ENSP00000423670.2, ENST00000506585.6
      Conserved Domains (1) summary
      cd00086
      Location:381 → 437
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    2. NM_001177479.2 → NP_001170950.1  highly divergent homeobox isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL022160, AL035552, BC143522, DA719263
      Consensus CDS
      CCDS35342.1
      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7
      Related
      ENSP00000362272.2, ENST00000373177.3
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:439 → 495
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    3. NM_144657.5 → NP_653258.2  highly divergent homeobox isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and represents use of an alternate promoter, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL035552, BC101720, DA719263
      Consensus CDS
      CCDS35342.1
      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7
      Related
      ENSP00000297977.5, ENST00000297977.9
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:439 → 495
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      84317878..84502453 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029275.2 → XP_016884764.1  highly divergent homeobox isoform X2

      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:421 → 477
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    2. XM_017029274.2 → XP_016884763.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:439 → 495
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    3. XM_047441827.1 → XP_047297783.1  highly divergent homeobox isoform X2

    4. XM_011530864.2 → XP_011529166.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:439 → 495
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    5. XM_047441828.1 → XP_047297784.1  highly divergent homeobox isoform X2

    6. XM_011530863.3 → XP_011529165.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:439 → 495
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

    7. XM_047441829.1 → XP_047297785.1  highly divergent homeobox isoform X3

    RNA

    1. XR_001755653.2 RNA Sequence

    2. XR_001755652.2 RNA Sequence

    3. XR_938392.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      82754225..82938810 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326473.1 → XP_054182448.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7

    2. XM_054326474.1 → XP_054182449.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7

    3. XM_054326475.1 → XP_054182450.1  highly divergent homeobox isoform X2

    4. XM_054326476.1 → XP_054182451.1  highly divergent homeobox isoform X2

    5. XM_054326477.1 → XP_054182452.1  highly divergent homeobox isoform X2

    6. XM_054326472.1 → XP_054182447.1  highly divergent homeobox isoform X1

      UniProtKB/Swiss-Prot
      A8K1Y5, B7ZL18, Q5JZB4, Q7Z353, Q96NK7

    7. XM_054326478.1 → XP_054182453.1  highly divergent homeobox isoform X3

    RNA

    1. XR_008485453.1 RNA Sequence

    2. XR_008485451.1 RNA Sequence

    3. XR_008485452.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z353.1 GenPept UniProtKB/Swiss-Prot:Q7Z353

    Gene LinkOut

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

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