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    PLXDC1 plexin domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 57125, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PLXDC1provided by HGNC
    Official Full Name
    plexin domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20945
    See related
    Ensembl:ENSG00000161381 MIM:606826; AllianceGenome:HGNC:20945
    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
    TEM3; TEM7
    Summary
    Predicted to be involved in spinal cord development. Part of receptor complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in gall bladder (RPKM 7.4), endometrium (RPKM 6.4) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLXDC1 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39063313..39152967, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (39927167..40015495, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37219566..37307890, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371767 Neighboring gene long intergenic non-protein coding RNA 2079 Neighboring gene leucine rich repeat containing 37 member A11, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:37202329-37203528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8447 Neighboring gene RDM1 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37228227-37229015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37239721-37240221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37243560-37244060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37255200-37255801 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37265163-37265351 Neighboring gene uncharacterized LOC124903995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37309916-37310422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37310423-37310927 Neighboring gene tRNA-Cys (anticodon GCA) 2-3 Neighboring gene tRNA-Cys (anticodon GCA) 2-4

    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. High expression of tumor endothelial marker 7 is associated with metastasis and poor survival of patients with osteogenic sarcoma. Fuchs B, et al. Gene, 2007 Sep 15. PMID 17560052, Free PMC Article
    2. TEM7 (PLXDC1) in neovascular endothelial cells of fibrovascular membranes from patients with proliferative diabetic retinopathy. Yamaji Y, et al. Invest Ophthalmol Vis Sci, 2008 Jul. PMID 18316703
    3. Preferential expression of the secreted and membrane forms of tumor endothelial marker 7 transcripts in osteosarcoma. Halder C, et al. Anticancer Res, 2009 Nov. PMID 20032373, Free PMC Article
    4. Glioblastoma endothelium drives bevacizumab-induced infiltrative growth via modulation of PLXDC1. Falchetti ML, et al. Int J Cancer, 2019 Mar 15. PMID 30414187, Free PMC Article
    5. Tumor endothelial marker 7 (TEM-7): a novel target for antiangiogenic therapy. Bagley RG, et al. Microvasc Res, 2011 Nov. PMID 21958527

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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).
    2. Serum TEM5 and TEM7 concentrations correlate with clinicopathologic features and poor prognosis of colorectal cancer patients
      Title: Serum TEM5 and TEM7 concentrations correlate with clinicopathologic features and poor prognosis of colorectal cancer patients.
    3. Study revealed that over-expression of PLXDC1 per se was able to change partly the growth features of U87MG glioblastoma cells. Molecularly, PLXDC1 regulated the epithelial to mesenchymal transition program of tumor cells, whereby its silencing increased the mRNA levels of epithelial transcripts, whereas those of mesenchymal marker genes were reduced.
      Title: Glioblastoma endothelium drives bevacizumab-induced infiltrative growth via modulation of PLXDC1.
    4. PLXDC1 silencing by the HA-CH-NP/siRNA significantly inhibited tumor growth in A2780 tumor-bearing mice.
      Title: Selective delivery of PLXDC1 small interfering RNA to endothelial cells for anti-angiogenesis tumor therapy using CD44-targeted chitosan nanoparticles for epithelial ovarian cancer.
    5. Immunohistochemical analysis of 122 gliomas showed that TGLI1 expression was positively correlated with VEGF-C, TEM7 and microvessel density.
      Title: The gain-of-function GLI1 transcription factor TGLI1 enhances expression of VEGF-C and TEM7 to promote glioblastoma angiogenesis.
    6. 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.
    7. TEM-7 is a vascular protein associated with angiogenic states. TEM-7 is a novel and attractive target for antiangiogenic therapy.
      Title: Tumor endothelial marker 7 (TEM-7): a novel target for antiangiogenic therapy.
    8. 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.
    9. All osteosarcoma cell lines, 6/9 tumors but none of the bone specimens expressed mRNA of TEM7 secreted forms 1 and 2.
      Title: Preferential expression of the secreted and membrane forms of tumor endothelial marker 7 transcripts in osteosarcoma.
    10. TEM7 may play significant role in proliferation and maintenance of neovascular endothelial cells in fibrovascular membranes. TEM7 may be molecular target for new diagnostic and therapeutic strategies for proliferative diabetic retinopathy.
      Title: TEM7 (PLXDC1) in neovascular endothelial cells of fibrovascular membranes from patients with proliferative diabetic retinopathy.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    • FLJ36270, FLJ45632, DKFZp686F0937

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in angiogenesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spinal cord development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in bicellular tight junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular space NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    plexin domain-containing protein 1
    Names
    2410003I07Rik
    tumor endothelial marker 3
    tumor endothelial marker 7

    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_020405.5 → NP_065138.2  plexin domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_065138.2

      Status: VALIDATED

      Source sequence(s)
      AC091178, AF378753, AK312999, BC036059, DA205327
      Consensus CDS
      CCDS11333.1
      UniProtKB/Swiss-Prot
      B2R7I8, Q5QCZ7, Q5QCZ8, Q5QCZ9, Q8IUK5, Q9HCT9
      UniProtKB/TrEMBL
      B4E173
      Related
      ENSP00000323927.4, ENST00000315392.9
      Conserved Domains (3) summary
      pfam01437
      Location:303 → 347
      PSI; Plexin repeat
      pfam05283
      Location:303 → 441
      MGC-24; Multi-glycosylated core protein 24 (MGC-24), sialomucin
      cl02648
      Location:152 → 242
      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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      39063313..39152967 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436434.1 → XP_047292390.1  plexin domain-containing protein 1 isoform X15

    2. XM_047436432.1 → XP_047292388.1  plexin domain-containing protein 1 isoform X14

    3. XM_047436435.1 → XP_047292391.1  plexin domain-containing protein 1 isoform X15

      Related
      ENSP00000409687.2, ENST00000444911.6

    4. XM_047436428.1 → XP_047292384.1  plexin domain-containing protein 1 isoform X5

    5. XM_047436427.1 → XP_047292383.1  plexin domain-containing protein 1 isoform X4

    6. XM_047436426.1 → XP_047292382.1  plexin domain-containing protein 1 isoform X3

    7. XM_047436425.1 → XP_047292381.1  plexin domain-containing protein 1 isoform X2

    8. XM_047436424.1 → XP_047292380.1  plexin domain-containing protein 1 isoform X1

    9. XM_047436429.1 → XP_047292385.1  plexin domain-containing protein 1 isoform X6

    10. XM_047436431.1 → XP_047292387.1  plexin domain-containing protein 1 isoform X8

    11. XM_047436433.1 → XP_047292389.1  plexin domain-containing protein 1 isoform X9

    12. XM_047436436.1 → XP_047292392.1  plexin domain-containing protein 1 isoform X10

    13. XM_047436430.1 → XP_047292386.1  plexin domain-containing protein 1 isoform X7

    14. XM_047436437.1 → XP_047292393.1  plexin domain-containing protein 1 isoform X11

    15. XM_047436438.1 → XP_047292394.1  plexin domain-containing protein 1 isoform X12

    16. XM_047436439.1 → XP_047292395.1  plexin domain-containing protein 1 isoform X13

      Related
      ENSP00000462089.1, ENST00000578390.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      39927167..40015495 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316715.1 → XP_054172690.1  plexin domain-containing protein 1 isoform X5

    2. XM_054316714.1 → XP_054172689.1  plexin domain-containing protein 1 isoform X4

    3. XM_054316713.1 → XP_054172688.1  plexin domain-containing protein 1 isoform X3

    4. XM_054316712.1 → XP_054172687.1  plexin domain-containing protein 1 isoform X2

    5. XM_054316711.1 → XP_054172686.1  plexin domain-containing protein 1 isoform X1

    6. XM_054316716.1 → XP_054172691.1  plexin domain-containing protein 1 isoform X6

    7. XM_054316718.1 → XP_054172693.1  plexin domain-containing protein 1 isoform X8

    8. XM_054316719.1 → XP_054172694.1  plexin domain-containing protein 1 isoform X9

    9. XM_054316720.1 → XP_054172695.1  plexin domain-containing protein 1 isoform X10

    10. XM_054316717.1 → XP_054172692.1  plexin domain-containing protein 1 isoform X7

    11. XM_054316721.1 → XP_054172696.1  plexin domain-containing protein 1 isoform X11

    12. XM_054316722.1 → XP_054172697.1  plexin domain-containing protein 1 isoform X12

    13. XM_054316723.1 → XP_054172698.1  plexin domain-containing protein 1 isoform X13

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IUK5.2 GenPept UniProtKB/Swiss-Prot:Q8IUK5

    Gene LinkOut

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

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