Vax1 ventral anterior homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Vax1provided by RGD
Full Name: ventral anterior homeobox 1provided by RGD
Primary source: RGD:621132
See related: Ensembl:ENSRNOG00000008824 AllianceGenome:RGD:621132
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 activity and DNA-binding transcription repressor activity, RNA polymerase II-specific. Predicted to be involved in central nervous system development; neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of transcription by RNA polymerase II; nervous system development; and skeletal muscle cell differentiation. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in syndromic microphthalmia 11. Orthologous to human VAX1 (ventral anterior homeobox 1). [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:: 1q55

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (268310644..268326713, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (258324571..258342396, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (280334897..280338813, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	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 DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 intronic transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin 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
acts_upstream_of_or_within astrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroepithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron migration	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 roof of mouth development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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: ventral anterior homeobox 1

Names: ventral anterior homeobox containing gene 1

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_022636.1 → NP_072158.1 ventral anterior homeobox 1

See identical proteins and their annotated locations for NP_072158.1

Status: PROVISIONAL

Source sequence(s)

AF113515

UniProtKB/Swiss-Prot

Q9JM00

UniProtKB/TrEMBL

A6JI80

Related

ENSRNOP00000011743.1, ENSRNOT00000011743.3

Conserved Domains (1) summary

pfam00046
Location:103 → 156

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_086019.1 Reference GRCr8

Range

268310644..268326713 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089683.2 → XP_038945611.1 ventral anterior homeobox 1 isoform X1

Conserved Domains (1) summary

pfam00046
Location:25 → 79

Homeobox; Homeobox domain
XM_039089676.2 → XP_038945604.1 ventral anterior homeobox 1 isoform X1

Conserved Domains (1) summary

pfam00046
Location:25 → 79

Homeobox; Homeobox domain