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Crx cone-rod homeobox [ Mus musculus (house mouse) ]

Gene ID: 12951, updated on 18-Sep-2024

Summary

Official Symbol
Crxprovided by MGI
Official Full Name
cone-rod homeoboxprovided by MGI
Primary source
MGI:MGI:1194883
See related
Ensembl:ENSMUSG00000041578 AllianceGenome:MGI:1194883
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Crx1
Summary
Enables several functions, including DNA-binding transcription factor activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and nuclear receptor binding activity. Involved in regulation of transcription, DNA-templated. Acts upstream of or within positive regulation of transcription by RNA polymerase II and retina development in camera-type eye. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including eye; face; and nervous system. Used to study Leber congenital amaurosis 7. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 7 and cone-rod dystrophy 2. Orthologous to human CRX (cone-rod homeobox). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See Crx in Genome Data Viewer
Location:
7 A2; 7 8.6 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (15599872..15613880, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (15865947..15879955, complement)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene oocyte specific homeobox 5 Neighboring gene STARR-seq mESC enhancer starr_18112 Neighboring gene oocyte specific homeobox 6 Neighboring gene STARR-seq mESC enhancer starr_18113 Neighboring gene STARR-seq mESC enhancer starr_18114 Neighboring gene STARR-seq mESC enhancer starr_18115 Neighboring gene cone-rod homeobox, opposite strand Neighboring gene argininosuccinate synthetase pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data 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

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription activator activity ISS
Inferred from Sequence or Structural Similarity
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 IDA
Inferred from Direct Assay
more info
PubMed 
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 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 ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables leucine zipper domain binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclear receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
cone-rod homeobox protein
Names
cone-rod homeobox containing

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)

  1. NM_001113330.1NP_001106801.1  cone-rod homeobox protein isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains a different 5' end exon compared to transcript variant 1 and initiates translation from an in-frame, upstream AUG, resulting in a longer isoform (2) with an unique N-terminus compared to isoform 1.
    Source sequence(s)
    AK139691, BC016502
    Consensus CDS
    CCDS52035.1
    UniProtKB/TrEMBL
    A0A0A0MQN6
    Related
    ENSMUSP00000134400.3, ENSMUST00000174318.8
    Conserved Domains (2) summary
    pfam00046
    Location:67117
    Homeobox; Homeobox domain
    pfam03529
    Location:188273
    TF_Otx; Otx1 transcription factor
  2. NM_007770.4NP_031796.1  cone-rod homeobox protein isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the more predominant transcript and encodes the shorter isoform (1)
    Source sequence(s)
    BC016502, BG403985
    Consensus CDS
    CCDS20840.1
    UniProtKB/Swiss-Prot
    O54751
    UniProtKB/TrEMBL
    Q543C9
    Related
    ENSMUSP00000043436.7, ENSMUST00000044434.13
    Conserved Domains (2) summary
    pfam00046
    Location:4393
    Homeobox; Homeobox domain
    pfam03529
    Location:164249
    TF_Otx; Otx1 transcription factor

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    15599872..15613880 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)