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Crxos cone-rod homeobox, opposite strand [ Mus musculus (house mouse) ]

Gene ID: 546024, updated on 11-Apr-2024

Summary

Official Symbol
Crxosprovided by MGI
Official Full Name
cone-rod homeobox, opposite strandprovided by MGI
Primary source
MGI:MGI:2451355
See related
Ensembl:ENSMUSG00000074365 AllianceGenome:MGI:2451355
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
Egam1; Crxos1
Summary
Predicted to enable transcription cis-regulatory region binding activity. Acts upstream of or within blastocyst hatching. Predicted to be active in nucleus. Is expressed in central nervous system; early conceptus; and retina. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
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Genomic context

See Crxos in Genome Data Viewer
Location:
7 A2; 7 8.6 cM
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (15616542..15637945)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (15882617..15904030)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene oocyte specific homeobox 6 Neighboring gene STARR-seq mESC enhancer starr_18112 Neighboring gene STARR-seq mESC enhancer starr_18113 Neighboring gene cone-rod homeobox Neighboring gene STARR-seq mESC enhancer starr_18114 Neighboring gene STARR-seq mESC enhancer starr_18115 Neighboring gene argininosuccinate synthetase pseudogene 1 Neighboring gene STARR-positive B cell enhancer ABC_E2813 Neighboring gene selenoprotein W

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)
  • Endonuclease-mediated (1) 

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
homeobox protein Crxos
Names
Crx opposite strand transcript 1
cone-rod homeobox, opposite strand protein
expressing gene at morula stage protein 1

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_001033638.3NP_001028810.1  homeobox protein Crxos isoform a

    See identical proteins and their annotated locations for NP_001028810.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also known as Egam1).
    Source sequence(s)
    AC148990
    Consensus CDS
    CCDS20841.1
    UniProtKB/Swiss-Prot
    B6ZND8, B6ZND9, Q3UL53
    Related
    ENSMUST00000098801.9
    Conserved Domains (2) summary
    cd00086
    Location:127179
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam00046
    Location:2061
    Homeobox; Homeobox domain
  2. NM_001145190.3NP_001138662.1  homeobox protein Crxos isoform b

    See identical proteins and their annotated locations for NP_001138662.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b, also known as Egam1C) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC148990
    Consensus CDS
    CCDS57498.1
    Related
    ENSMUST00000171280.3
    Conserved Domains (1) summary
    cd00086
    Location:2375
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  3. NM_001205274.2NP_001192203.1  homeobox protein Crxos isoform c

    See identical proteins and their annotated locations for NP_001192203.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (c, also known as Egam1N) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AC148990
    Consensus CDS
    CCDS57497.1
    Related
    ENSMUST00000150050.3
    Conserved Domains (1) summary
    pfam00046
    Location:2061
    Homeobox; Homeobox domain

RNA

  1. NR_038092.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC148990
    Related
    ENSMUST00000125993.8

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
    15616542..15637945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)