Otx2 orthodenticle homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Otx2provided by RGD
Full Name: orthodenticle homeobox 2provided by RGD
Primary source: RGD:1305705
See related: EnsemblRapid:ENSRNOG00000065063 AllianceGenome:RGD:1305705
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 activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including axon guidance; positive regulation of DNA-templated transcription; and positive regulation of gastrulation. Predicted to act upstream of or within several processes, including cellular response to leukemia inhibitory factor; nervous system development; and regionalization. Predicted to be located in cytoplasm; growth cone; and nucleus. Predicted to be part of transcription regulator complex. Human ortholog(s) of this gene implicated in panhypopituitarism and syndromic microphthalmia 5. Orthologous to human OTX2 (orthodenticle homeobox 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Restricted expression toward (RPKM 8.8) See more
Orthologs: human mouse all
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Genomic context

Location:: 15p14

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (24422876..24432709, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (21942233..21953034, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (25500037..25511619, complement)

Chromosome 15 - NC_086033.1 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?

Otx2 is a potential target for gene therapy of retinal degenerative diseases.
Title: Otx2 enhances transdifferentiation of Müller cells-derived retinal stem cells into photoreceptor-like cells.
The results suggest that Otx2 and Crx, both alone and in combination, act to control pineal melatonin synthesis.
Title: Homeobox genes in melatonin-producing pinealocytes: Otx2 and Crx act to promote hormone synthesis in the mature rat pineal gland.
Otx2S is a novel variant of the Otx2 gene with a deletion within the homeodomain sequence. OTX2S exerts transdominant activity on the tyrosinase promoter when tested in the physiological environment of primary retinal pigmented epithelial cells.
Title: Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells.
Otx2, the expression of which is developmentally confined to the regions anterior to the isthmus, is a factor responsible for the anterior-posterior region-dependent opposite effects of the bHLH proteins.
Title: Contrasting and brain region-specific roles of neurogenin2 and mash1 in GABAergic neuron differentiation in vitro.
the results suggest a novel role of Otx2 in thalamic cell migration
Title: GABA immunoreactivity in the developing rat thalamus and Otx2 homeoprotein expression in migrating neurons.

Submit: New GeneRIF Correction

General gene information

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Markers

Otx2 (e-PCR), detects polymorphism
- UniSTS:530694

OTX2_1019 (e-PCR)
- UniSTS:277547

OTX2_V273 (e-PCR)
- UniSTS:277547

Otx2 (e-PCR), detects polymorphism
- UniSTS:516143

Otx2 (e-PCR), detects polymorphism
- UniSTS:516144

BB256399 (e-PCR)
- UniSTS:209023

PMC304098P1 (e-PCR)
- UniSTS:272520

PMC263842P1 (e-PCR)
- UniSTS:272330

RH136748 (e-PCR)
- UniSTS:218837

Otx2 (e-PCR), detects polymorphism
- UniSTS:144106

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-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
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within diencephalon morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in dopaminergic neuron differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within eye photoreceptor cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of mesendoderm development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within metencephalon development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within midbrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroepithelial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate determination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of embryonic development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gastrulation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within primitive streak formation	ISO Inferred from Sequence Orthology more info
involved_in primitive streak formation	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	IEA Inferred from Electronic Annotation more info
involved_in protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somite rostral/caudal axis specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within telencephalon regionalization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in growth cone	IEA Inferred from Electronic Annotation more info
located_in growth cone	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein OTX2

Names: homeobox Otx2; homeobox protein OTX2-like; orthodenticle homolog 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_001100566.1 → NP_001094036.1 homeobox protein OTX2

See identical proteins and their annotated locations for NP_001094036.1

Status: PROVISIONAL

Source sequence(s)

CB580080, JAXUCZ010000015

UniProtKB/TrEMBL

A6KE75, F2Z3S7

Related

ENSRNOP00000073390.1, ENSRNOT00000085910.3

Conserved Domains (2) summary

pfam00046
Location:42 → 94

Homeobox; Homeobox domain

pfam03529
Location:155 → 234

TF_Otx; Otx1 transcription factor
NM_001431421.1 → NP_001418350.1 homeobox protein OTX2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A6KE75, F2Z3S7
NM_001431422.1 → NP_001418351.1 homeobox protein OTX2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A6KE75, F2Z3S7

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_086033.1 Reference GRCr8

Range

24422876..24432709 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039093283.2 → XP_038949211.1 homeobox protein OTX2 isoform X1

UniProtKB/TrEMBL

M0R4H6

Related

ENSRNOP00000064262.3, ENSRNOT00000074488.4

Conserved Domains (2) summary

pfam00046
Location:50 → 102

Homeobox; Homeobox domain

pfam03529
Location:163 → 242

TF_Otx; Otx1 transcription factor
XM_006251838.5 → XP_006251900.1 homeobox protein OTX2 isoform X2

Conserved Domains (2) summary

pfam00046
Location:42 → 94

Homeobox; Homeobox domain

pfam03529
Location:155 → 234

TF_Otx; Otx1 transcription factor
XM_039093285.2 → XP_038949213.1 homeobox protein OTX2 isoform X2

Conserved Domains (2) summary

pfam00046
Location:42 → 94

Homeobox; Homeobox domain

pfam03529
Location:155 → 234

TF_Otx; Otx1 transcription factor
XM_063274232.1 → XP_063130302.1 homeobox protein OTX2 isoform X2

UniProtKB/TrEMBL

A6KE75, F2Z3S7