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Otx1 orthodenticle homeobox 1 [ Mus musculus (house mouse) ]

Gene ID: 18423, updated on 11-Sep-2019

Summary

Official Symbol
Otx1provided by MGI
Official Full Name
orthodenticle homeobox 1provided by MGI
Primary source
MGI:MGI:97450
See related
Ensembl:ENSMUSG00000005917
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
jv; A730044F23Rik
Summary
This gene encodes a member of the bicoid subfamily of the paired homeobox transcription factor family. The encoded protein is critical to the maintenance and regionalization of the forebrain and midbrain during development. It may also have important functions in sense organ development, pituitary function, and in the regulation of blood cell production. [provided by RefSeq, Jul 2008]
Expression
Biased expression in CNS E11.5 (RPKM 7.7), CNS E14 (RPKM 4.1) and 5 other tissues See more
Orthologs

Genomic context

See Otx1 in Genome Data Viewer
Location:
11 A3.2; 11 14.1 cM
Exon count:
5
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (21994764..22001651, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (21894767..21901654, complement)

Chromosome 11 - NC_000077.6Genomic Context describing neighboring genes Neighboring gene ribosomal protein L15, pseudogene 1 Neighboring gene ferritin light chain 1 pseudogene Neighboring gene predicted gene, 32517 Neighboring gene EH domain binding protein 1 Neighboring gene predicted gene, 51938 Neighboring gene DnaJ (Hsp40) homolog, subfamily A, member 1 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
anterior/posterior pattern specification IGI
Inferred from Genetic Interaction
more info
PubMed 
diencephalon morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
forebrain development IGI
Inferred from Genetic Interaction
more info
PubMed 
inner ear morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
metencephalon development IGI
Inferred from Genetic Interaction
more info
PubMed 
midbrain development IGI
Inferred from Genetic Interaction
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IC
Inferred by Curator
more info
PubMed 

General protein information

Preferred Names
homeobox protein OTX1
Names
orthodenticle homolog 1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_011023.3NP_035153.1  homeobox protein OTX1

    See identical proteins and their annotated locations for NP_035153.1

    Status: REVIEWED

    Source sequence(s)
    BB652255, BC057105, BC058354
    Consensus CDS
    CCDS24468.1
    UniProtKB/Swiss-Prot
    P80205
    UniProtKB/TrEMBL
    Q5SS54
    Related
    ENSMUSP00000006071.7, ENSMUST00000006071.13
    Conserved Domains (2) summary
    pfam00046
    Location:4294
    Homeobox; Homeobox domain
    pfam03529
    Location:178274
    TF_Otx; Otx1 transcription factor

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000077.6 Reference GRCm38.p6 C57BL/6J

    Range
    21994764..22001651 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030245654.1XP_030101514.1  homeobox protein OTX1 isoform X1

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