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    LYPD1 LY6/PLAUR domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 116372, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LYPD1provided by HGNC
    Official Full Name
    LY6/PLAUR domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28431
    See related
    Ensembl:ENSG00000150551 MIM:610450; AllianceGenome:HGNC:28431
    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
    PHTS; LYPDC1
    Summary
    Predicted to enable acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to act upstream of or within several processes, including behavioral fear response; cholinergic synaptic transmission; and negative regulation of protein localization to plasma membrane. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 4.3), colon (RPKM 1.3) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPD1 in Genome Data Viewer
    Location:
    2q21.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (132643286..132671526, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (133081646..133109877, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (133400859..133429099, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor 39 Neighboring gene RN7SK pseudogene 103 Neighboring gene Y-box binding protein 1 pseudogene 7 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:133362908-133363464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:133426641-133427604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16540 Neighboring gene NCK associated protein 5 Neighboring gene Sharpr-MPRA regulatory region 3189 Neighboring gene uncharacterized LOC112268439 Neighboring gene NCKAP5 antisense RNA 1

    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. ALKBH5 suppresses malignancy of hepatocellular carcinoma via m(6)A-guided epigenetic inhibition of LYPD1. Chen Y, et al. Mol Cancer, 2020 Aug 10. PMID 32772918, Free PMC Article
    2. PHTS, a novel putative tumor suppressor, is involved in the transformation reversion of HeLaHF cells independently of the p53 pathway. Yu DH, et al. Exp Cell Res, 2006 Apr 1. PMID 16413018
    3. Identification of GPI-anchored protein LYPD1 as an essential factor for odontoblast differentiation in tooth development. Fu Y, et al. J Biol Chem, 2023 May. PMID 36963497, Free PMC Article
    4. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877
    5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ALKBH5 suppresses malignancy of hepatocellular carcinoma via m(6)A-guided epigenetic inhibition of LYPD1.
      Title: ALKBH5 suppresses malignancy of hepatocellular carcinoma via m(6)A-guided epigenetic inhibition of LYPD1.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. The PHTS is involved in HeLaHF reversion independently of the p53 pathway, and Expression profiling revealed that PHTS is one of the genes that is up-regulated in HeLaHF but not in HeLa.
      Title: PHTS, a novel putative tumor suppressor, is involved in the transformation reversion of HeLaHF cells independently of the p53 pathway.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ41033, MGC29643

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylcholine receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acetylcholine receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in behavioral fear response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to nicotine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic transmission, cholinergic IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ly6/PLAUR domain-containing protein 1
    Names
    putative HeLa tumor suppressor

    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_001077427.4 → NP_001070895.1  ly6/PLAUR domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001070895.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a different segment for its 5' UTR and 5' coding region, compared to variant 1. This results in translation initiation at a downstream AUG and a protein (isoform b) with a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC079773, AK094501, AK309668, AW014835
      Consensus CDS
      CCDS46416.1
      UniProtKB/TrEMBL
      Q53RU6
      Related
      ENSP00000340563.6, ENST00000345008.6

    2. NM_001321234.2 → NP_001308163.1  ly6/PLAUR domain-containing protein 1 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC079773, AK130005, AW014835
      UniProtKB/Swiss-Prot
      Q8N2G4

    3. NM_001321235.2 → NP_001308164.1  ly6/PLAUR domain-containing protein 1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC010974, AC079773, AW014835, BP276862
      Consensus CDS
      CCDS46416.1
      UniProtKB/TrEMBL
      Q53RU6

    4. NM_144586.7 → NP_653187.3  ly6/PLAUR domain-containing protein 1 isoform a precursor

      See identical proteins and their annotated locations for NP_653187.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform a).
      Source sequence(s)
      AC010974, AC079773, AW014835, BC017318
      Consensus CDS
      CCDS42759.1
      UniProtKB/Swiss-Prot
      H7BXW6, Q6ZP52, Q6ZWI4, Q8N2G4, Q96AC2
      Related
      ENSP00000380605.2, ENST00000397463.3

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      132643286..132671526 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      133081646..133109877 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N2G4.2 GenPept UniProtKB/Swiss-Prot:Q8N2G4

    Gene LinkOut

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

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