LYPD3 LY6/PLAUR domain containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LYPD3provided by HGNC
Official Full Name: LY6/PLAUR domain containing 3provided by HGNC
Primary source: HGNC:HGNC:24880
See related: Ensembl:ENSG00000124466 MIM:609484; AllianceGenome:HGNC:24880
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: C4.4A
Summary: Predicted to enable laminin binding activity. Involved in negative regulation of smooth muscle cell apoptotic process. Located in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in esophagus (RPKM 319.1) and skin (RPKM 226.0) See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (43460787..43465608, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (46281130..46285954, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (43964939..43969760, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

m6A-dependent mature miR-151-5p accelerates the malignant process of HNSCC by targeting LYPD3.
Title: m6A-dependent mature miR-151-5p accelerates the malignant process of HNSCC by targeting LYPD3.
LY6/PLAUR domain containing 3 (LYPD3) maintains melanoma cell stemness and mediates an immunosuppressive microenvironment.
Title: LY6/PLAUR domain containing 3 (LYPD3) maintains melanoma cell stemness and mediates an immunosuppressive microenvironment.
The authors explored the related pathways through which LYPD3 affects the pathogenesis and prognosis of lung adenocarcinoma by gene set enrichment analysis, and found that LYPD3 might affect the clinical manifestations of lung adenocarcinoma by regulating the P53 signaling pathway.
Title: Elevated Expression of LYPD3 Is Associated with Lung Adenocarcinoma Carcinogenesis and Poor Prognosis.
Long non-coding RNA OGFRP1 contributed to progression of non-small cell lung cancer at least partly through upregulating LYPD3 expression by sponging miR-124-3p.
Title: Long non-coding RNA OGFRP1 regulates LYPD3 expression by sponging miR-124-3p and promotes non-small cell lung cancer progression.
While in the healthy liver hepatocytes are C4.4A negative, data show that C4.4A is strongly expressed in hepatocellular carcinoma (HCC) with upregulation at the invasive front and in lung metastasis, indicating that C4.4A apparently contributes to HCC progression.
Title: De novo synthesis of C4.4A in hepatocellular carcinoma promotes migration and invasion of tumor cells.
Our results are consistent with previous data in mouse embryogenesis and wound healing. Based on these findings, we conclude that this human TES model provides an excellent surrogate for studies of C4.4A and Haldisin expressions in human stratified epithelia.
Title: Expression of C4.4A in an In Vitro Human Tissue-Engineered Skin Model.
Expression and crystallographic studies of the D1D2 domains of C4.4A have been reported.
Title: Expression and crystallographic studies of the D1D2 domains of C4.4A, a homologous protein to the urokinase receptor.
LYPD3 has a role in the maintenance of colorectal cancer stem-like cells.
Title: LY6/PLAUR domain containing 3 has a role in the maintenance of colorectal cancer stem-like cells.
Highly expressed C4.4A protein in HER2-positive human breast cancers indicate a good prognosis.
Title: C4.4A highly expressed in HER2-positive human breast cancers may indicate a good prognosis.
overexpression of C4.4A correlates with metastatic potential of gastric cancer and C4.4A could be a novel independent prognostic marker for predicting outcome.
Title: Expression of C4.4A is a potential independent prognostic factor for patients with gastric cancer.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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
The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

STS-D29356 (e-PCR)
- UniSTS:35931

STS-W72299 (e-PCR)
- UniSTS:23943

STS-T69460 (e-PCR)
- UniSTS:24797

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables laminin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of smooth muscle cell apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed
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 3

Names: 2310061G07Rik; GPI-anchored metastasis-associated protein C4.4A homolog; GPI-anchored metastasis-associated protein homolog; MIG-C4; matrigel-induced gene C4 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)

NM_014400.3 → NP_055215.2 ly6/PLAUR domain-containing protein 3 precursor

See identical proteins and their annotated locations for NP_055215.2

Status: VALIDATED

Source sequence(s)

AC018758, BC039167, BP367221, DA837818

Consensus CDS

CCDS12620.1

UniProtKB/Swiss-Prot

O95274, Q9UJ74

UniProtKB/TrEMBL

A8K4E0, B2RBR3

Related

ENSP00000244333.2, ENST00000244333.4

Conserved Domains (2) summary

cd00117
Location:31 → 116

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 ...

pfam00021
Location:140 → 222

UPAR_LY6; u-PAR/Ly-6 domain