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    Hdx highly divergent homeobox [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317617, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Hdxprovided by RGD
    Official Full Name
    highly divergent homeoboxprovided by RGD
    Primary source
    RGD:1563666
    See related
    EnsemblRapid:ENSRNOG00000037799 AllianceGenome:RGD:1563666
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1563666
    Summary
    Predicted to enable DNA binding activity. Predicted to be located in nucleus. Orthologous to human HDX (highly divergent homeobox). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 31.8), Lung (RPKM 24.4) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hdx in Genome Data Viewer
    Location:
    Xq31
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (80739615..80881621, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (76552539..76697177, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (82847895..83151516, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene transfer RNA arginine (anticodon CCU) 9 Neighboring gene ribosomal protein S6 kinase A6 Neighboring gene CWC22 spliceosome associated protein homolog, pseudogene 2 Neighboring gene serine and arginine rich splicing factor 10, pseudogene 1 Neighboring gene testis expressed gene 16 Neighboring gene ubiquitin-conjugating enzyme E2D 4 like 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    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.

    mRNA and Protein(s)

    1. NM_001395571.1 → NP_001382500.1  highly divergent homeobox isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A0G2KAK4
      Related
      ENSRNOP00000108636.1, ENSRNOT00000168677.1
      Conserved Domains (2) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain
      cd00086
      Location:441 → 497
      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_001395572.1 → NP_001382501.1  highly divergent homeobox isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A0G2KAK4, D4A457
      Related
      ENSRNOP00000075430.4, ENSRNOT00000077587.4
      Conserved Domains (1) summary
      cd00086
      Location:383 → 439
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      80739615..80881621 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039099856.2 → XP_038955784.1  highly divergent homeobox isoform X1

      Conserved Domains (1) summary
      smart00389
      Location:4 → 59
      HOX; Homeodomain

    RNA

    1. XR_005498000.2 RNA Sequence

    2. XR_005498003.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001134568.1: Suppressed sequence

      Description
      NM_001134568.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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