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

Gene ID: 147719, updated on 5-Mar-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. Predicted to be anchored component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 27.7) See more
Orthologs
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Genomic context

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Location:
19q13.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (41835075..41844871, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (44653180..44664338, complement)
105.20220307 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)

Genotypes

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_2023_10

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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