Format

Send to:

Choose Destination
    • Showing Current items.

    cdh4 cadherin 4, type 1, R-cadherin (retinal) [ Danio rerio (zebrafish) ]

    Gene ID: 30297, updated on 14-Feb-2019

    Summary

    Official Symbol
    cdh4provided by ZNC
    Official Full Name
    cadherin 4, type 1, R-cadherin (retinal)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-991207-1
    See related
    Ensembl:ENSDARG00000015002
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
    Also known as
    rcad; R-cadherin; zgc:136316

    Genomic context

    See cdh4 in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (20371182..20826753)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (20269870..20725441)
    103 previous assembly Zv9 (GCF_000002035.4) 11 NC_007122.5 (20746612..21202183)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108191636 Neighboring gene opioid growth factor receptor-like 2 Neighboring gene zgc:162182 Neighboring gene uncharacterized LOC110440098 Neighboring gene TAF4A RNA polymerase II, TATA box binding protein (TBP)-associated factor

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    General gene information

    Homology

    Clone Names

    • MGC158132

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    cytoskeletal protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    adherens junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    camera-type eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell adhesion mediated by cadherin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cranial nerve development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    lateral line system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of eye photoreceptor cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    retina morphogenesis in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    cadherin-4
    Names
    cadherin 4, retinal

    NCBI Reference Sequences (RefSeq)

    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_001045273.2NP_001038738.2  cadherin-4 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001038738.2

      Status: PROVISIONAL

      Description
      Transcript Variant: This variant (2) lacks numerous exons and transcription extends through a splice site in the 5' coding that results in a novel 3' coding region and 3' UTR, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC135069
      UniProtKB/TrEMBL
      A4IGF0
      Related
      ENSDARP00000094797.3, ENSDART00000104022.4
      Conserved Domains (1) summary
      cl07391
      Location:3357
      Cadherin_pro; Cadherin prodomain like
    2. NM_131086.2NP_571161.2  cadherin-4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_571161.2

      Status: PROVISIONAL

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      BC129136
      UniProtKB/TrEMBL
      A1L1M6
      Related
      ENSDARP00000134356.1, ENSDART00000164982.2
      Conserved Domains (5) summary
      cd11304
      Location:295402
      Cadherin_repeat; Cadherin tandem repeat domain
      smart01055
      Location:34128
      Cadherin_pro; Cadherin prodomain like
      pfam00028
      Location:632726
      Cadherin; Cadherin domain
      pfam01049
      Location:784926
      Cadherin_C; Cadherin cytoplasmic region
      cl09101
      Location:187287
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007122.7 Reference GRCz11 Primary Assembly

      Range
      20371182..20826753
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394816.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      49754..53395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_3

    Genomic

    1. NW_018395385.1 Reference GRCz11 ALT_DRER_TU_3

      Range
      292133..295741
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center