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Hoxd1 homeo box D1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 288151, updated on 2-Nov-2024

Summary

Official Symbol
Hoxd1provided by RGD
Official Full Name
homeo box D1provided by RGD
Primary source
RGD:1309179
See related
EnsemblRapid:ENSRNOG00000001572 AllianceGenome:RGD:1309179
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 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 act upstream of or within embryonic skeletal system development; neuron differentiation; and sensory perception of pain. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXD1 (homeobox D1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See Hoxd1 in Genome Data Viewer
Location:
3q23
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (80073041..80075180)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (59665629..59667769)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (61685619..61687758)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene homeo box D3 Neighboring gene uncharacterized LOC120101574 Neighboring gene uncharacterized LOC134486290 Neighboring gene metaxin 2

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Gene Ontology Provided by RGD

Process Evidence Code Pubs
acts_upstream_of_or_within embryonic skeletal system development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within neuron differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within sensory perception of pain ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
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.

mRNA and Protein(s)

  1. NM_001105884.1NP_001099354.1  homeobox protein Hox-D1

    See identical proteins and their annotated locations for NP_001099354.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473949
    UniProtKB/TrEMBL
    A6HME0, D4ACE4
    Related
    ENSRNOP00000002140.4, ENSRNOT00000002140.6
    Conserved Domains (2) summary
    COG5576
    Location:208325
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:233285
    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
    80073041..80075180
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)