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    cdhr1a cadherin-related family member 1a [ Danio rerio (zebrafish) ]

    Gene ID: 449008, updated on 2-Nov-2024

    Summary

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    Official Symbol
    cdhr1aprovided by ZNC
    Official Full Name
    cadherin-related family member 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040924-4
    See related
    Ensembl:ENSDARG00000004643 AllianceGenome:ZFIN:ZDB-GENE-040924-4
    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
    cdhr1; pcdh21
    Summary
    Predicted to enable calcium ion binding activity. Involved in retina layer formation. Acts upstream of or within glial cell development and retina development in camera-type eye. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in retinal outer nuclear layer. Human ortholog(s) of this gene implicated in cone-rod dystrophy 15. Orthologous to human CDHR1 (cadherin related family member 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See cdhr1a in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (29480656..29505601, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (29350206..29375204, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene leucine-rich repeat, immunoglobulin-like and transmembrane domains 1a Neighboring gene leucine-rich repeat, immunoglobulin-like and transmembrane domains 2 Neighboring gene carbohydrate (chondroitin 6) sulfotransferase 3a Neighboring gene uncharacterized LOC137487410

    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. Proteasome-Mediated Regulation of Cdhr1a by Siah1 Modulates Photoreceptor Development and Survival in Zebrafish. Piedade WP, et al. Front Cell Dev Biol, 2020. PMID 33330480, Free PMC Article
    2. Proteolytic shedding of the extracellular domain of photoreceptor cadherin. Implications for outer segment assembly. Rattner A, et al. J Biol Chem, 2004 Oct 1. PMID 15284225
    3. Genetic control of cellular morphogenesis in Müller glia. Charlton-Perkins M, et al. Glia, 2019 Jul. PMID 30924555, Free PMC Article
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within glial cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retina layer formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-related family member 1a
    Names
    cadherin-related family member 1
    photoreceptor cadherin
    prCAD
    protocadherin-21

    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_001005402.1 → NP_001005402.1  cadherin-related family member 1a precursor

      See identical proteins and their annotated locations for NP_001005402.1

      Status: PROVISIONAL

      Source sequence(s)
      AY684930
      UniProtKB/Swiss-Prot
      Q6B3P0
      Related
      ENSDARP00000101442.2, ENSDART00000110005.4
      Conserved Domains (2) summary
      cd11304
      Location:146 → 247
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam15048
      Location:714 → 754
      OSTbeta; Organic solute transporter subunit beta protein

    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_007124.7 Reference GRCz11 Primary Assembly

      Range
      29480656..29505601 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005156820.5 → XP_005156877.1  cadherin-related family member 1a isoform X1

      UniProtKB/TrEMBL
      A0A8M2B2V7, G1K2I7
      Related
      ENSDARP00000026292.7, ENSDART00000026679.8
      Conserved Domains (2) summary
      cd11304
      Location:144 → 245
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam15048
      Location:712 → 752
      OSTbeta; Organic solute transporter subunit beta protein

    2. XM_068212835.1 → XP_068068936.1  cadherin-related family member 1a isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6B3P0.1 GenPept UniProtKB/Swiss-Prot:Q6B3P0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.