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cdx1a caudal type homeobox 1a [ Danio rerio (zebrafish) ]

Gene ID: 405762, updated on 28-Oct-2024

Summary

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Official Symbol
cdx1aprovided by ZNC
Official Full Name
caudal type homeobox 1aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-050510-1
See related
Ensembl:ENSDARG00000114554 AllianceGenome:ZFIN:ZDB-GENE-050510-1
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
cdx2
Summary
Predicted to enable DNA-binding transcription factor activity and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including anterior/posterior pattern specification; heart formation; and retinoic acid receptor signaling pathway. Predicted to be active in nucleus. Is expressed in several structures, including intestinal bulb; margin; mesoderm; neuroectoderm; and tail bud. Orthologous to human CDX1 (caudal type homeobox 1). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs
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Genomic context

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See cdx1a in Genome Data Viewer
Location:
chromosome: 14
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 14 NC_007125.7 (3288382..3311533)
105 previous assembly GRCz10 (GCF_000002035.5) Unplaced Scaffold NW_003335281.1 (20213..25785, complement)

Chromosome 14 - NC_007125.7Genomic Context describing neighboring genes Neighboring gene colony stimulating factor 1 receptor, a Neighboring gene platelet-derived growth factor receptor, beta polypeptide Neighboring gene uncharacterized LOC110440201 Neighboring gene uncharacterized LOC110437825

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Identification of in vivo Hox13-binding sites reveals an essential locus controlling zebrafish brachyury expression. Ye Z, et al. Development, 2021 Jun 1. PMID 34061173, Free PMC Article
  2. Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88. Cheesman SE, et al. Proc Natl Acad Sci U S A, 2011 Mar 15. PMID 20921418, Free PMC Article
  3. Intestinal differentiation in zebrafish requires Cdx1b, a functional equivalent of mammalian Cdx2. Flores MV, et al. Gastroenterology, 2008 Nov. PMID 18804112
  4. Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. Siegel N, et al. BMC Genomics, 2007 Sep 6. PMID 17822543, Free PMC Article
  5. Interactions between Cdx genes and retinoic acid modulate early cardiogenesis. Lengerke C, et al. Dev Biol, 2011 Jun 1. PMID 21466798, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Repression of the hindbrain developmental program by Cdx factors is required for the specification of the vertebrate spinal cord.
    Title: Repression of the hindbrain developmental program by Cdx factors is required for the specification of the vertebrate spinal cord.
  2. The expression and function of cdx1a are reported.
    Title: The caudal-related homeobox genes cdx1a and cdx4 act redundantly to regulate hox gene expression and the formation of putative hematopoietic stem cells during zebrafish embryogenesis.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity 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 transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in anterior/posterior axis specification IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within anterior/posterior axis specification IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within anterior/posterior pattern specification IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in digestive tract development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in embryonic pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within heart formation IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within hemopoiesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within hindbrain-spinal cord boundary formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within pancreas development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within pronephros development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
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 retinoic acid receptor signaling pathway IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within rostrocaudal neural tube patterning IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within somitogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 CDX-1a
Names
caudal type homeo box transcription factor 1 a
homeobox protein Cdx2

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_212836.3 → NP_998001.2  homeobox protein CDX-1a

    See identical proteins and their annotated locations for NP_998001.2

    Status: PROVISIONAL

    Source sequence(s)
    BC115217
    UniProtKB/TrEMBL
    A0A2R8QGG2, A4FUM9, Q8AXR4
    Related
    ENSDARP00000151122.1, ENSDART00000186290.1
    Conserved Domains (3) summary
    COG5576
    Location:122 → 227
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:133 → 185
    Homeobox; Homeobox domain
    pfam04731
    Location:11 → 115
    Caudal_act; Caudal like protein activation region

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007125.7 Reference GRCz11 Primary Assembly

    Range
    3288382..3311533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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