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    PLXDC2 plexin domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 84898, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PLXDC2provided by HGNC
    Official Full Name
    plexin domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:21013
    See related
    Ensembl:ENSG00000120594 MIM:606827; AllianceGenome:HGNC:21013
    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
    TEM7R; PLXDC2-OT
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in gall bladder (RPKM 10.7), lung (RPKM 7.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLXDC2 in Genome Data Viewer
    Location:
    10p12.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (19816432..20289856)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (19834692..20308236)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (20105361..20578785)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902388 Neighboring gene RNA, U6 small nuclear 1212, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:20104285-20105050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:20208919-20209420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3118 Neighboring gene NANOG hESC enhancer GRCh37_chr10:20408149-20408686 Neighboring gene NANOG hESC enhancer GRCh37_chr10:20413464-20413975 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:20546341-20546868 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:20659563-20660207 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:20661486-20662107 Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:20716465-20716965 Neighboring gene microRNA 4675

    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. The Upregulation of PLXDC2 Correlates with Immune Microenvironment Characteristics and Predicts Prognosis in Gastric Cancer. Li Y, et al. Dis Markers, 2021. PMID 34777633, Free PMC Article
    2. Plexin domain containing protein 2 is more expressed within the invasive area of human colorectal cancer tissues. Hamada Y, et al. Hum Cell, 2021 Sep. PMID 34146255
    3. Genetic Variant Near PLXDC2 Influences the Risk of Primary Open-angle Glaucoma by Increasing Intraocular Pressure in the Japanese Population. Mabuchi F, et al. J Glaucoma, 2017 Nov. PMID 28930887
    4. Plexin domain containing 2 (PLXDC2) gene polymorphism rs7081455 may not influence POAG risk in a Saudi cohort. Kondkar AA, et al. BMC Res Notes, 2018 Oct 16. PMID 30326957, Free PMC Article
    5. Expression Pattern of Plexin Domain Containing 2 in Human Hepatocellular Carcinoma. Yamamoto N, et al. Monoclon Antib Immunodiagn Immunother, 2020 Apr. PMID 32202949

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Adaptive c-Met-PLXDC2 Signaling Axis Mediates Cancer Stem Cell Plasticity to Confer Radioresistance-associated Aggressiveness in Head and Neck Cancer.
      Title: Adaptive c-Met-PLXDC2 Signaling Axis Mediates Cancer Stem Cell Plasticity to Confer Radioresistance-associated Aggressiveness in Head and Neck Cancer.
    2. The Upregulation of PLXDC2 Correlates with Immune Microenvironment Characteristics and Predicts Prognosis in Gastric Cancer.
      Title: The Upregulation of PLXDC2 Correlates with Immune Microenvironment Characteristics and Predicts Prognosis in Gastric Cancer.
    3. Plexin domain containing protein 2 is more expressed within the invasive area of human colorectal cancer tissues.
      Title: Plexin domain containing protein 2 is more expressed within the invasive area of human colorectal cancer tissues.
    4. Plxdc family members are novel receptors for the rhesus monkey rhadinovirus (RRV).
      Title: Plxdc family members are novel receptors for the rhesus monkey rhadinovirus (RRV).
    5. Expression Pattern of Plexin Domain Containing 2 in Human Hepatocellular Carcinoma.
      Title: Expression Pattern of Plexin Domain Containing 2 in Human Hepatocellular Carcinoma.
    6. A Genome Wide Association Study on plasma FV levels identified PLXDC2 as a new modifier of the coagulation process.
      Title: A Genome Wide Association Study on plasma FV levels identified PLXDC2 as a new modifier of the coagulation process.
    7. PLXDC2 rs7081455 is not associated with primary open angle glaucoma or its clinical phenotypes in patients of Saudi origin.
      Title: Plexin domain containing 2 (PLXDC2) gene polymorphism rs7081455 may not influence POAG risk in a Saudi cohort.
    8. The genetic variant near the PLXDC2 gene was found to influence the risk of POAG by increasing IOP in the Japanese population.
      Title: Genetic Variant Near PLXDC2 Influences the Risk of Primary Open-angle Glaucoma by Increasing Intraocular Pressure in the Japanese Population.
    9. PLXDC1 and PLXDC2 as the transmembrane receptors for the multifunctional factor PEDF.
      Title: Identification of PLXDC1 and PLXDC2 as the transmembrane receptors for the multifunctional factor PEDF.
    10. We identified a genetic association for susceptibility to retinopathy in 5 novel chromosomal regions and PLXDC2 and ARHGAP22, the latter 2 of which are genes implicated in endothelial cell angiogenesis and increased capillary permeability.
      Title: Genome-wide association study of diabetic retinopathy in a Taiwanese population.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
    EBI GWAS Catalog
    Genome-wide association study of diabetic retinopathy in a Taiwanese population.
    EBI GWAS Catalog

    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

    • FLJ14623

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    plexin domain-containing protein 2
    Names
    1200007L24Rik
    tumor endothelial marker 7-related 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)

    1. NM_001282736.2 → NP_001269665.1  plexin domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001269665.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC067743, AI311457, AL353147, AL353790, AY358486, BC012885
      Consensus CDS
      CCDS60497.1
      UniProtKB/TrEMBL
      B4E367
      Related
      ENSP00000366450.3, ENST00000377242.7
      Conserved Domains (2) summary
      pfam01437
      Location:278 → 323
      PSI; Plexin repeat
      cl02648
      Location:142 → 233
      NIDO; Nidogen-like

    2. NM_032812.9 → NP_116201.7  plexin domain-containing protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_116201.7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC067743, AI311457, AL353147, AL353790, AY358486
      Consensus CDS
      CCDS7132.1
      UniProtKB/Swiss-Prot
      Q6UX71, Q96E59, Q96PD9, Q96SU9
      UniProtKB/TrEMBL
      B4E367
      Related
      ENSP00000366460.3, ENST00000377252.5
      Conserved Domains (2) summary
      pfam01437
      Location:327 → 372
      PSI; Plexin repeat
      cl02648
      Location:191 → 282
      NIDO; Nidogen-like

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      19816432..20289856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519750.3 → XP_011518052.1  plexin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B4E367
      Conserved Domains (2) summary
      pfam01437
      Location:327 → 372
      PSI; Plexin repeat
      cl02648
      Location:191 → 282
      NIDO; Nidogen-like

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      19834692..20308236
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367033.1 → XP_054223008.1  plexin domain-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UX71.1 GenPept UniProtKB/Swiss-Prot:Q6UX71

    Gene LinkOut

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

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
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