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Hoxd4 homeo box D4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 288153, updated on 2-Nov-2024

Summary

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Official Symbol
Hoxd4provided by RGD
Official Full Name
homeo box D4provided by RGD
Primary source
RGD:1309690
See related
EnsemblRapid:ENSRNOG00000001578 AllianceGenome:RGD:1309690
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within stem cell differentiation. Predicted to be located in cell junction. Predicted to be active in nucleoplasm. Orthologous to human HOXD4 (homeobox D4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Adrenal (RPKM 61.8), Kidney (RPKM 41.7) and 5 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Hoxd4 in Genome Data Viewer
Location:
3q23
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (80021886..80041462)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (59614464..59634042)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (61634005..61653581)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene homeo box D9 Neighboring gene uncharacterized LOC120101573 Neighboring gene homeobox D8 Neighboring gene microRNA 10b Neighboring gene homeo box D3 Neighboring gene uncharacterized LOC120101574

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 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. Mutations in paralogous Hox genes result in overlapping homeotic transformations of the axial skeleton: evidence for unique and redundant function. Horan GS, et al. Dev Biol, 1995 May. PMID 7750651
  2. Compound mutants for the paralogous hoxa-4, hoxb-4, and hoxd-4 genes show more complete homeotic transformations and a dose-dependent increase in the number of vertebrae transformed. Horan GS, et al. Genes Dev, 1995 Jul 1. PMID 7628700
  3. HOX4 genes encode transcription factors with potential auto- and cross-regulatory capacities. Zappavigna V, et al. EMBO J, 1991 Dec. PMID 1756725, Free PMC Article
  4. Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Nishiyama A, et al. Cell Stem Cell, 2009 Oct 2. PMID 19796622, Free PMC Article
  5. 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 transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
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
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within anterior/posterior pattern specification ISO
Inferred from Sequence Orthology
more info
  
involved_in embryonic organ development ISO
Inferred from Sequence Orthology
more info
  
involved_in embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within embryonic skeletal system morphogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within stem cell differentiation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cell junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell junction ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
homeobox protein Hox-D4

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_001105885.2 → NP_001099355.1  homeobox protein Hox-D4

    See identical proteins and their annotated locations for NP_001099355.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A6HMD5, D4ACE1
    Conserved Domains (1) summary
    pfam00046
    Location:155 → 209
    Homeobox; Homeobox domain

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_086021.1 Reference GRCr8

    Range
    80021886..80041462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039104415.2 → XP_038960343.1  homeobox protein Hox-D4 isoform X1

    UniProtKB/TrEMBL
    A6HMD5, D4ACE1
    Related
    ENSRNOP00000002145.3, ENSRNOT00000002145.8
    Conserved Domains (1) summary
    pfam00046
    Location:155 → 209
    Homeobox; Homeobox domain
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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