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    CDHR1 cadherin related family member 1 [ Homo sapiens (human) ]

    Gene ID: 92211, updated on 11-Apr-2024

    Summary

    Official Symbol
    CDHR1provided by HGNC
    Official Full Name
    cadherin related family member 1provided by HGNC
    Primary source
    HGNC:HGNC:14550
    See related
    Ensembl:ENSG00000148600 MIM:609502; AllianceGenome:HGNC:14550
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RP65; PRCAD; CORD15; PCDH21
    Summary
    This gene belongs to the cadherin superfamily of calcium-dependent cell adhesion molecules. The encoded protein is a photoreceptor-specific cadherin that plays a role in outer segment disc morphogenesis. Mutations in this gene are associated with inherited retinal dystrophies. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2013]
    Expression
    Biased expression in skin (RPKM 98.8), colon (RPKM 10.9) and 1 other tissue See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    10q23.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (84194537..84219621)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (85073058..85098147)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (85954293..85979377)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85931151-85931652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3677 Neighboring gene competing endogenous lncRNA 2 for microRNA let-7b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85936583-85937084 Neighboring gene G protein-coupled receptor 15 ligand Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:85939583-85940403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963048-85963548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963549-85964049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85974015-85974538 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 2 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1775, DKFZp434A132

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in photoreceptor cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in photoreceptor cell outer segment organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
     
    located_in photoreceptor outer segment membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    cadherin-related family member 1
    Names
    MT-protocadherin
    photoreceptor cadherin
    protocadherin-21

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_028034.1 RefSeqGene

      Range
      4882..29039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171971.3NP_001165442.1  cadherin-related family member 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001165442.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB593154, AC022389, BC038799
      Consensus CDS
      CCDS53548.1
      UniProtKB/Swiss-Prot
      Q96JP9
      UniProtKB/TrEMBL
      F1T0L2
      Related
      ENSP00000331063.3, ENST00000332904.7
      Conserved Domains (1) summary
      cd11304
      Location:139241
      Cadherin_repeat; Cadherin tandem repeat domain
    2. NM_033100.4NP_149091.1  cadherin-related family member 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_149091.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA576346, AB593154, AB593155, AC022389, BM674749
      Consensus CDS
      CCDS7372.1
      UniProtKB/Swiss-Prot
      Q69YZ8, Q8IXY5, Q96JP9
      UniProtKB/TrEMBL
      F1T0L2
      Related
      ENSP00000485478.1, ENST00000623527.4
      Conserved Domains (1) summary
      cd11304
      Location:139241
      Cadherin_repeat; Cadherin tandem repeat domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      84194537..84219621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011540338.2XP_011538640.1  cadherin-related family member 1 isoform X2

      Conserved Domains (1) summary
      cd11304
      Location:197299
      Cadherin_repeat; Cadherin tandem repeat domain
    2. XM_011540337.2XP_011538639.1  cadherin-related family member 1 isoform X1

      Conserved Domains (1) summary
      cd11304
      Location:197299
      Cadherin_repeat; Cadherin tandem repeat domain
    3. XM_011540340.4XP_011538642.1  cadherin-related family member 1 isoform X4

      Conserved Domains (1) summary
      cd11304
      Location:197299
      Cadherin_repeat; Cadherin tandem repeat domain
    4. XM_047425997.1XP_047281953.1  cadherin-related family member 1 isoform X5

      Related
      ENSP00000361189.4, ENST00000372117.6
    5. XM_011540339.2XP_011538641.1  cadherin-related family member 1 isoform X3

      Conserved Domains (1) summary
      cd11304
      Location:328423
      Cadherin_repeat; Cadherin tandem repeat domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      85073058..85098147
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367145.1XP_054223120.1  cadherin-related family member 1 isoform X1

    2. XM_054367146.1XP_054223121.1  cadherin-related family member 1 isoform X2

    3. XM_054367148.1XP_054223123.1  cadherin-related family member 1 isoform X4

    4. XM_054367149.1XP_054223124.1  cadherin-related family member 1 isoform X5

    5. XM_054367147.1XP_054223122.1  cadherin-related family member 1 isoform X3