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

Summary

Official Symbol: Hoxd1provided by RGD
Official Full Name: homeo box D1provided by RGD
Primary source: RGD:1309179
See related: Ensembl: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, Apr 2022]
Expression: Low expression observed in reference dataset See more
Orthologs: human mouse all
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Genomic context

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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

Hoxd1 (e-PCR), detects polymorphism
- UniSTS:536666

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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 sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

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

General protein information

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Preferred Names: homeobox protein Hox-D1

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)

NM_001105884.1 → NP_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, ENSRNOT00000002140.5

Conserved Domains (2) summary

COG5576
Location:208 → 325

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:233 → 285

Homeobox; Homeobox domain