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

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 RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; chromatin binding activity; and nuclear receptor binding activity. Involved in regulation of DNA-templated transcription. 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 face; liver; lung; nervous system; and retina. Used to study Leber congenital amaurosis 7 and cone-rod dystrophy 2. 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, Dec 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

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_000073.7 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors.
Title: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors.
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms.
Title: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms.
Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development.
Title: Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development.
CRX gene could induce the differentiation of Muller cell-derived progenitor into rod photoreceptors, indicating a new avenue to study muller cells as endogenous seed cells for retinal photoreceptor
Title: [Exogenous CRX gene induces Müller cell-derived progenitors to differentiate into photoreceptors].
A Crx-dependent gene regulatory network was unraveled involving presynaptic genes that encode cytomatrix-associated proteins governing the organization of the photoreceptor ribbon synapse but not the formation of ribbon structure.
Title: Cone-rod homeobox CRX controls presynaptic active zone formation in photoreceptors of mammalian retina.
Results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.
Title: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo.
CRX is required for chromatin remodeling at only a subset of its binding sites, which undergo retina or neuronal specific activation during photoreceptor differentiation.
Title: CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites.
proteins involved in phototransduction were not detected in the Crx(-/-) mouse; in this phenotype, however, proteins from spots showing diurnal rhythms were specifically identified as enzymes involved in glucose metabolism, Krebs cycle, and mitochondrial enzymes.
Title: Diurnal expression of proteins in the retina of the blind cone-rod homeobox (Crx(-/-) ) mouse and the 129/Sv mouse: a proteomic study.
The L253X mouse provides a valuable model for CRX-associated retinopathy. The pathogenicity of CRX frameshift mutations depends on the position of the premature termination codon, which in turn determines the degree of mutant mRNA/protein overproduction.
Title: Crx-L253X Mutation Produces Dominant Photoreceptor Defects in TVRM65 Mice.
CRX-associated retinopathies stem from graded changes in photoreceptor gene expression, which could significantly contribute to phenotypic variability.
Title: Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Variation

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Alleles

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

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (4) 1 citation
Spontaneous (2) 1 citation
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Crx (e-PCR), detects polymorphism
- UniSTS:234038

U77615 (e-PCR)
- UniSTS:179518

116J6.1 (e-PCR), detects polymorphism
- UniSTS:243329

Crx (e-PCR), detects polymorphism
- UniSTS:536452

Crx (e-PCR), detects polymorphism
- UniSTS:536453

Crx (e-PCR), detects polymorphism
- UniSTS:546710

Crx (e-PCR), detects polymorphism
- UniSTS:527024

Crx (e-PCR), detects polymorphism
- UniSTS:527025

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

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation 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

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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)

NM_001113330.1 → NP_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:67 → 117

Homeobox; Homeobox domain

pfam03529
Location:188 → 273

TF_Otx; Otx1 transcription factor
NM_007770.4 → NP_031796.1 cone-rod homeobox protein isoform 1

See identical proteins and their annotated locations for NP_031796.1

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:43 → 93

Homeobox; Homeobox domain

pfam03529
Location:164 → 249

TF_Otx; Otx1 transcription factor