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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
    all
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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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