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

Summary

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

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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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

UniSTS:480790 (e-PCR)
- UniSTS:480790

Hoxd4 (e-PCR), detects polymorphism
- UniSTS:536672

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)

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

NC_086021.1 Reference GRCr8

Range

80021886..80041462

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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