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    CDHR4 cadherin related family member 4 [ Homo sapiens (human) ]

    Gene ID: 389118, updated on 12-Sep-2024

    Summary

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    Official Symbol
    CDHR4provided by HGNC
    Official Full Name
    cadherin related family member 4provided by HGNC
    Primary source
    HGNC:HGNC:34527
    See related
    Ensembl:ENSG00000187492 AllianceGenome:HGNC:34527
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDH29; PRO34300
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in lung (RPKM 3.2), testis (RPKM 2.4) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3p21.31
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49790732..49802914, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49820605..49832790, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49828165..49837306, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene inositol hexakisphosphate kinase 1 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 14 Neighboring gene PHF5A pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49823653-49824342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19875 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:49824674-49824838 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:49825619-49825828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14375 Neighboring gene Sharpr-MPRA regulatory region 10954 Neighboring gene inka box actin regulator 1 Neighboring gene microRNA 5193 Neighboring gene ubiquitin like modifier activating enzyme 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Association analysis of 3p21 with Crohn's disease in a New Zealand population. Morgan AR, et al. Hum Immunol, 2010 Jun. PMID 20307617
    2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article
    3. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association analysis of 3p21 with Crohn's disease in a New Zealand population.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC164982

    Gene Ontology Provided by GOA

    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
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-related family member 4
    Names
    Cadherin-like protein UNQ9392/PRO34300
    VLLR9392
    cadherin-like 29
    cadherin-like protein 29

    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_001007540.4 → NP_001007541.2  cadherin-related family member 4 precursor

      See identical proteins and their annotated locations for NP_001007541.2

      Status: VALIDATED

      Source sequence(s)
      AC139451, AY358221, BC146674, DR008129
      Consensus CDS
      CCDS46829.1
      UniProtKB/Swiss-Prot
      A6H8M9, Q6UXT0
      Related
      ENSP00000391409.2, ENST00000412678.7
      Conserved Domains (1) summary
      cd11304
      Location:447 → 546
      Cadherin_repeat; Cadherin tandem repeat domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      49790732..49802914 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533701.3 → XP_011532003.1  cadherin-related family member 4 isoform X4

      See identical proteins and their annotated locations for XP_011532003.1

      Conserved Domains (1) summary
      cd11304
      Location:447 → 546
      Cadherin_repeat; Cadherin tandem repeat domain

    2. XM_017006367.1 → XP_016861856.1  cadherin-related family member 4 isoform X1

      Conserved Domains (1) summary
      cd11304
      Location:499 → 598
      Cadherin_repeat; Cadherin tandem repeat domain

    3. XM_017006369.1 → XP_016861858.1  cadherin-related family member 4 isoform X3

      Conserved Domains (1) summary
      cd11304
      Location:494 → 593
      Cadherin_repeat; Cadherin tandem repeat domain

    4. XM_017006368.1 → XP_016861857.1  cadherin-related family member 4 isoform X2

      Conserved Domains (1) summary
      cd11304
      Location:499 → 598
      Cadherin_repeat; Cadherin tandem repeat domain

    5. XM_017006366.1 → XP_016861855.1  cadherin-related family member 4 isoform X1

      Conserved Domains (1) summary
      cd11304
      Location:499 → 598
      Cadherin_repeat; Cadherin tandem repeat domain

    6. XM_011533700.4 → XP_011532002.1  cadherin-related family member 4 isoform X4

      See identical proteins and their annotated locations for XP_011532002.1

      Conserved Domains (1) summary
      cd11304
      Location:447 → 546
      Cadherin_repeat; Cadherin tandem repeat domain

    7. XM_017006370.1 → XP_016861859.1  cadherin-related family member 4 isoform X5

    8. XM_017006371.1 → XP_016861860.1  cadherin-related family member 4 isoform X5

    RNA

    1. XR_001740143.1 RNA Sequence

    2. XR_007095677.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      49820605..49832790 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346471.1 → XP_054202446.1  cadherin-related family member 4 isoform X4

    2. XM_054346468.1 → XP_054202443.1  cadherin-related family member 4 isoform X1

    3. XM_054346470.1 → XP_054202445.1  cadherin-related family member 4 isoform X3

    4. XM_054346469.1 → XP_054202444.1  cadherin-related family member 4 isoform X2

    5. XM_054346467.1 → XP_054202442.1  cadherin-related family member 4 isoform X1

    6. XM_054346472.1 → XP_054202447.1  cadherin-related family member 4 isoform X4

    7. XM_054346473.1 → XP_054202448.1  cadherin-related family member 4 isoform X5

    8. XM_054346474.1 → XP_054202449.1  cadherin-related family member 4 isoform X5

    RNA

    1. XR_008486716.1 RNA Sequence

    2. XR_008486715.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6H8M9.1 GenPept UniProtKB/Swiss-Prot:A6H8M9

    Gene LinkOut

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