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

Gene ID: 116372, updated on 5-Mar-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 binding activity and 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 membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 4.3), colon (RPKM 1.3) and 16 other tissues See more
Orthologs
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Genomic context

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Location:
2q21.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (132643286..132671526, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (133081646..133109877, complement)
105.20220307 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
  • 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
  
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_2023_10

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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