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    LYPD4 LY6/PLAUR domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 147719, updated on 9-Dec-2024

    Summary

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    Official Symbol
    LYPD4provided by HGNC
    Official Full Name
    LY6/PLAUR domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:28659
    See related
    Ensembl:ENSG00000273111 AllianceGenome:HGNC:28659
    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
    SMR
    Summary
    Predicted to be located in extracellular region and plasma membrane. Predicted to be active in plasma membrane raft. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward testis (RPKM 27.7) See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPD4 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (41835075..41844871, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (44653180..44664338, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (42341148..42348746, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CEA cell adhesion molecule 3 Neighboring gene CEA cell adhesion molecule 1 pseudogene Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 52 Neighboring gene DMRT like family C2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:42364028-42364783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10673 Neighboring gene ribosomal protein S19 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:42373545-42374103 Neighboring gene microRNA 6797

    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. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. Daakour S, et al. BMC Cancer, 2016 May 26. PMID 27229929, Free PMC Article
    2. Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, et al. Science, 2008 Feb 15. PMID 18187620
    3. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
    4. 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
    5. The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. Capalbo L, et al. Nat Commun, 2019 Oct 4. PMID 31586073, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of LY6/PLAUR domain containing 4 (LYPD4) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC42718, AC020956.3

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in plasma membrane raft IBA
    Inferred from Biological aspect of Ancestor
    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 4
    Names
    sperm membrane receptor
    testicular tissue protein Li 159

    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_001291419.2 → NP_001278348.1  ly6/PLAUR domain-containing protein 4 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001278348.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the 5' UTR and coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC243967, BC034629
      Consensus CDS
      CCDS77303.1
      UniProtKB/Swiss-Prot
      Q6UWN0
      Related
      ENSP00000339568.4, ENST00000343055.5
      Conserved Domains (1) summary
      pfam00021
      Location:107 → 177
      UPAR_LY6; u-PAR/Ly-6 domain

    2. NM_173506.7 → NP_775777.3  ly6/PLAUR domain-containing protein 4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_775777.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC243967, AK292305, BC034629
      Consensus CDS
      CCDS12587.1
      UniProtKB/Swiss-Prot
      Q6UWN0, Q8IYW0
      UniProtKB/TrEMBL
      A8K8E0
      Related
      ENSP00000476510.1, ENST00000609812.6
      Conserved Domains (1) summary
      pfam00021
      Location:142 → 212
      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
      41835075..41844871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451375.2 → XP_024307143.1  ly6/PLAUR domain-containing protein 4 isoform X5

      Conserved Domains (1) summary
      pfam00021
      Location:142 → 212
      UPAR_LY6; u-PAR/Ly-6 domain

    2. XM_005278385.6 → XP_005278442.1  ly6/PLAUR domain-containing protein 4 isoform X3

      Conserved Domains (1) summary
      pfam00021
      Location:155 → 225
      UPAR_LY6; u-PAR/Ly-6 domain

    3. XM_024451378.2 → XP_024307146.1  ly6/PLAUR domain-containing protein 4 isoform X7

      Conserved Domains (1) summary
      cl10471
      Location:142 → 179
      LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

    4. XM_024451373.2 → XP_024307141.1  ly6/PLAUR domain-containing protein 4 isoform X4

      UniProtKB/Swiss-Prot
      Q6UWN0, Q8IYW0
      UniProtKB/TrEMBL
      A8K8E0
      Conserved Domains (1) summary
      pfam00021
      Location:142 → 212
      UPAR_LY6; u-PAR/Ly-6 domain

    5. XM_006723035.3 → XP_006723098.1  ly6/PLAUR domain-containing protein 4 isoform X2

      Conserved Domains (1) summary
      pfam00021
      Location:151 → 221
      UPAR_LY6; u-PAR/Ly-6 domain

    6. XM_005258543.3 → XP_005258600.1  ly6/PLAUR domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005258600.1

      Conserved Domains (1) summary
      pfam00021
      Location:155 → 225
      UPAR_LY6; u-PAR/Ly-6 domain

    7. XM_005278388.5 → XP_005278445.1  ly6/PLAUR domain-containing protein 4 isoform X8

      See identical proteins and their annotated locations for XP_005278445.1

      Conserved Domains (1) summary
      pfam00021
      Location:93 → 163
      UPAR_LY6; u-PAR/Ly-6 domain

    8. XM_024451376.2 → XP_024307144.1  ly6/PLAUR domain-containing protein 4 isoform X7

      Conserved Domains (1) summary
      cl10471
      Location:142 → 179
      LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

    9. XM_005278387.6 → XP_005278444.1  ly6/PLAUR domain-containing protein 4 isoform X6

      Conserved Domains (1) summary
      cl10471
      Location:155 → 192
      LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

    10. XM_005278383.6 → XP_005278440.1  ly6/PLAUR domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005278440.1

      Conserved Domains (1) summary
      pfam00021
      Location:155 → 225
      UPAR_LY6; u-PAR/Ly-6 domain

    11. XM_011526483.2 → XP_011524785.1  ly6/PLAUR domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011524785.1

      Conserved Domains (1) summary
      pfam00021
      Location:155 → 225
      UPAR_LY6; u-PAR/Ly-6 domain

    12. XM_011526484.3 → XP_011524786.1  ly6/PLAUR domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011524786.1

      Conserved Domains (1) summary
      pfam00021
      Location:155 → 225
      UPAR_LY6; u-PAR/Ly-6 domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      44653180..44664338 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319871.1 → XP_054175846.1  ly6/PLAUR domain-containing protein 4 isoform X5

    2. XM_054319869.1 → XP_054175844.1  ly6/PLAUR domain-containing protein 4 isoform X3

    3. XM_054319874.1 → XP_054175849.1  ly6/PLAUR domain-containing protein 4 isoform X7

    4. XM_054319870.1 → XP_054175845.1  ly6/PLAUR domain-containing protein 4 isoform X4

      UniProtKB/Swiss-Prot
      Q6UWN0, Q8IYW0
      UniProtKB/TrEMBL
      A8K8E0

    5. XM_054319868.1 → XP_054175843.1  ly6/PLAUR domain-containing protein 4 isoform X2

    6. XM_054319865.1 → XP_054175840.1  ly6/PLAUR domain-containing protein 4 isoform X1

    7. XM_054319875.1 → XP_054175850.1  ly6/PLAUR domain-containing protein 4 isoform X8

    8. XM_054319873.1 → XP_054175848.1  ly6/PLAUR domain-containing protein 4 isoform X7

    9. XM_054319872.1 → XP_054175847.1  ly6/PLAUR domain-containing protein 4 isoform X6

    10. XM_054319864.1 → XP_054175839.1  ly6/PLAUR domain-containing protein 4 isoform X1

    11. XM_054319866.1 → XP_054175841.1  ly6/PLAUR domain-containing protein 4 isoform X1

    12. XM_054319867.1 → XP_054175842.1  ly6/PLAUR domain-containing protein 4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWN0.2 GenPept UniProtKB/Swiss-Prot:Q6UWN0

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