Shox2 SHOX homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Shox2provided by RGD
Official Full Name: SHOX homeobox 2provided by RGD
Primary source: RGD:3674
See related: EnsemblRapid:ENSRNOG00000012478 AllianceGenome:RGD:3674
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 transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including heart development; positive regulation of cell development; and regulation of branching morphogenesis of a nerve. Predicted to act upstream of or within several processes, including animal organ development; embryonic forelimb morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in lung cancer. Orthologous to human SHOX2 (short stature homeobox 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 18.8), Muscle (RPKM 15.3) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (153524324..153537571, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (151217049..151227180, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (164118175..164126783, complement)

Chromosome 2 - NC_086020.1 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?

important role in the process of intervertebral disc degeneration
Title: Role of SHOX2 in the development of intervertebral disc degeneration.

Submit: New GeneRIF Correction

General gene information

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Markers

AU026166 (e-PCR)
- UniSTS:114548

SGC44267 (e-PCR)
- UniSTS:41936

Shox2 (e-PCR), detects polymorphism
- UniSTS:498407

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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 factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cardiac atrium morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cardiac pacemaker cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cardiac right atrium morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cardiac right atrium morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cartilage development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chondrocyte development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in embryonic digestive tract morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic digestive tract morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic skeletal joint morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic skeletal joint morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart valve development	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of mesenchymal cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in muscle tissue morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in muscle tissue morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of axonogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mesenchymal cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of mesenchymal cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of skeletal muscle fiber development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of skeletal muscle fiber development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of branching morphogenesis of a nerve	IEA Inferred from Electronic Annotation more info
involved_in regulation of branching morphogenesis of a nerve	ISO Inferred from Sequence Orthology more info
involved_in regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of heart rate	IEA Inferred from Electronic Annotation more info
acts_upstream_of regulation of heart rate	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
involved_in sinoatrial node cell development	IEA Inferred from Electronic Annotation more info
involved_in sinoatrial node cell development	ISO Inferred from Sequence Orthology more info
involved_in sinoatrial node development	ISO Inferred from Sequence Orthology more info
involved_in sinoatrial valve development	IEA Inferred from Electronic Annotation more info
involved_in sinoatrial valve development	ISO Inferred from Sequence Orthology more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of stem cell proliferation	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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: short stature homeobox protein 2

Names: paired family homeodomain protein Prx3; short stature homeobox 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_013028.2 → NP_037160.2 short stature homeobox protein 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A6J5K8, G3V7M9

Related

ENSRNOP00000016843.5, ENSRNOT00000016843.7

Conserved Domains (2) summary

pfam00046
Location:143 → 197

Homeobox; Homeobox domain

pfam03826
Location:311 → 327

OAR; OAR 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_086020.1 Reference GRCr8

Range

153524324..153537571 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039101799.2 → XP_038957727.1 short stature homeobox protein 2 isoform X1

UniProtKB/TrEMBL

A6J5K7

Conserved Domains (2) summary

pfam00046
Location:143 → 197

Homeobox; Homeobox domain

pfam03826
Location:299 → 315

OAR; OAR domain