Vax2 ventral anterior homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vax2provided by RGD
Official Full Name: ventral anterior homeobox 2provided by RGD
Primary source: RGD:621133
See related: EnsemblRapid:ENSRNOG00000013261 AllianceGenome:RGD:621133
Gene type: protein coding
RefSeq status: VALIDATED
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 forebrain development; neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including dorsal/ventral axis specification; eye development; and negative regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human VAX2 (ventral anterior homeobox 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 2.2), Liver (RPKM 2.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (117753180..117777242)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (116195528..116219597)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (115388839..115412515)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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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Markers

Vax2 (e-PCR), detects polymorphism
- UniSTS:527039

D4Mit32 (e-PCR), detects polymorphism
- UniSTS:240077

AU048170 (e-PCR)
- UniSTS:109802

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 DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in axonogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axonogenesis	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 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
involved_in dorsal/ventral axis specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral axis specification	ISO Inferred from Sequence Orthology more info
involved_in embryonic eye morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic eye morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in forebrain development	IEA Inferred from Electronic Annotation more info
involved_in forebrain development	ISO Inferred from Sequence Orthology more info
involved_in forebrain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ventral anterior homeobox 2

Names: ventral anterior homeobox containing gene 2

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_022637.3 → NP_072159.2 ventral anterior homeobox 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q9JLZ9

UniProtKB/TrEMBL

A6IAP0, G3V7R0

Related

ENSRNOP00000018128.1, ENSRNOT00000018128.4

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_086022.1 Reference GRCr8

Range

117753180..117777242

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108321.2 → XP_038964249.1 ventral anterior homeobox 2 isoform X1

Conserved Domains (1) summary

pfam00046
Location:2 → 41

Homeobox; Homeobox domain