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    LYPD5 LY6/PLAUR domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 284348, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LYPD5provided by HGNC
    Official Full Name
    LY6/PLAUR domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:26397
    See related
    Ensembl:ENSG00000159871 MIM:619618; AllianceGenome:HGNC:26397
    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
    PRO4356; HALDISIN
    Summary
    Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in skin (RPKM 12.1), brain (RPKM 2.5) and 5 other tissues See more
    Orthologs
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    Genomic context

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    See LYPD5 in Genome Data Viewer
    Location:
    19q13.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43795927..43820634, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46618728..46643530, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (44300079..44324786, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene SMG9 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10729 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44268619-44268844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14739 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44270408-44270571 Neighboring gene CRISPRi-validated cis-regulatory element KCNN4 K1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44281957-44282457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44283513-44284012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10731 Neighboring gene potassium calcium-activated channel subfamily N member 4 Neighboring gene CRISPRi-validated cis-regulatory element chr19.4589 Neighboring gene Sharpr-MPRA regulatory region 14970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44288851-44289352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44289353-44289852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14744 Neighboring gene zinc finger protein 283 Neighboring gene zinc finger protein 404

    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
    • 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. The urokinase receptor homolog Haldisin is a novel differentiation marker of stratum granulosum in squamous epithelia. Gårdsvoll H, et al. J Histochem Cytochem, 2013 Nov. PMID 23896969, Free PMC Article
    2. Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions. Kriegbaum MC, et al. J Histochem Cytochem, 2015 Feb. PMID 25414274, Free PMC Article
    3. The correlation between reading and mathematics ability at age twelve has a substantial genetic component. Davis OS, et al. Nat Commun, 2014 Jul 8. PMID 25003214, Free PMC Article
    4. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article
    5. A proteome-scale map of the SARS-CoV-2-human contactome. Kim DK, et al. Nat Biotechnol, 2023 Jan. PMID 36217029, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions
      Title: Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions.
    2. The study identifies LYPD5 a novel differentiation marker of stratum granulosum in squamous epithelia.
      Title: The urokinase receptor homolog Haldisin is a novel differentiation marker of stratum granulosum in squamous epithelia.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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

    EBI GWAS Catalog

    Description
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
    EBI GWAS Catalog

    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

    • FLJ30469

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ly6/PLAUR domain-containing protein 5
    Names
    human antigen with LU-domains expressed in skin
    metastasis-associated protein

    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_001031749.3 → NP_001026919.2  ly6/PLAUR domain-containing protein 5 isoform A precursor

      See identical proteins and their annotated locations for NP_001026919.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (A) encodes the longer protein (isoform A).
      Source sequence(s)
      AC115522, AY358719, BC044237, BC057816, CF529795, DC364960
      Consensus CDS
      CCDS46096.1
      UniProtKB/Swiss-Prot
      Q6PEX9, Q6UWN5, Q96DR2
      UniProtKB/TrEMBL
      B4DWV3
      Related
      ENSP00000367185.2, ENST00000377950.8
      Conserved Domains (1) summary
      pfam00021
      Location:135 → 214
      UPAR_LY6; u-PAR/Ly-6 domain

    2. NM_001288763.2 → NP_001275692.1  ly6/PLAUR domain-containing protein 5 isoform B

      See identical proteins and their annotated locations for NP_001275692.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (C) contains a distinct 5' UTR, lacks an in-frame portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded protein (isoform B) has a distinct N-terminus and is shorter than isoform A. Variants B and C encode the same protein.
      Source sequence(s)
      AC115522, BC044237, CF529795, CK823626, DA093306
      Consensus CDS
      CCDS12631.1
      UniProtKB/TrEMBL
      B4DWV3
      Related
      ENSP00000471692.1, ENST00000594013.5
      Conserved Domains (1) summary
      pfam00021
      Location:92 → 171
      UPAR_LY6; u-PAR/Ly-6 domain

    3. NM_182573.3 → NP_872379.2  ly6/PLAUR domain-containing protein 5 isoform B

      See identical proteins and their annotated locations for NP_872379.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (B) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The encoded protein (isoform B) has a distinct N-terminus and is shorter than isoform A. Variants B and C encode the same protein.
      Source sequence(s)
      AC115522, BC044237, CF529795, DA286806
      Consensus CDS
      CCDS12631.1
      UniProtKB/TrEMBL
      B4DWV3
      Related
      ENSP00000408433.1, ENST00000414615.6
      Conserved Domains (1) summary
      pfam00021
      Location:92 → 171
      UPAR_LY6; u-PAR/Ly-6 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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      43795927..43820634 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      46618728..46643530 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWN5.2 GenPept UniProtKB/Swiss-Prot:Q6UWN5

    Gene LinkOut

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

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