Otx1 orthodenticle homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Otx1provided by RGD
Full Name: orthodenticle homeobox 1provided by RGD
Primary source: RGD:3237
See related: Ensembl:ENSRNOG00000065081 AllianceGenome:RGD:3237
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
Also known as: OTX1X
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 positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within anterior/posterior pattern specification; brain development; and inner ear morphogenesis. Predicted to be active in nucleus. Orthologous to human OTX1 (orthodenticle homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 1.4), Lung (RPKM 0.3) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 14q22

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (100283406..100290421, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (96082146..96089161, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (106861556..106864933, complement)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

ventricular cells actively sequester Otx1 in the cytoplasm, either by preventing nuclear import or by promoting a balance of export over import signals.
Title: Regulated nuclear trafficking of the homeodomain protein otx1 in cortical neurons.

Submit: New GeneRIF Correction

General gene information

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Markers

Otx1 (e-PCR), detects polymorphism
- UniSTS:530693

Otx1 (e-PCR), detects polymorphism
- UniSTS:164914

Otx1 (e-PCR), detects polymorphism
- UniSTS:234049

RH131109 (e-PCR)
- UniSTS:214392

RH140938 (e-PCR)
- UniSTS:214392

UniSTS:470671 (e-PCR)
- UniSTS:470671

Otx1 (e-PCR), detects polymorphism
- UniSTS:470671

RH94705 (e-PCR)
- UniSTS:119952

Otx1 (e-PCR), detects polymorphism
- UniSTS:144101

Otx1 (e-PCR), detects polymorphism
- UniSTS:144102

Otx1 (e-PCR), detects polymorphism
- UniSTS:507882

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	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 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
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in diencephalon morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within diencephalon morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
involved_in inner ear morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in metencephalon development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within metencephalon development	ISO Inferred from Sequence Orthology more info
involved_in midbrain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within midbrain development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	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 regulation of transcription by RNA polymerase II	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: homeobox protein OTX1

Names: homeobox protein OTX1-like

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_013109.3 → NP_037241.2 homeobox protein OTX1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000014

UniProtKB/TrEMBL

A0A8I6AA41

Related

ENSRNOP00000088754.1, ENSRNOT00000113729.1

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_086032.1 Reference GRCr8

Range

100283406..100290421 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039091640.2 → XP_038947568.1 homeobox protein OTX1 isoform X1

UniProtKB/Swiss-Prot

Q63410, Q64203

UniProtKB/TrEMBL

A0A8I6AA41

Conserved Domains (2) summary

pfam00046
Location:42 → 95

Homeobox; Homeobox domain

pfam03529
Location:180 → 274

TF_Otx; Otx1 transcription factor