Aliases for PLXDC2 Gene

Aliases for PLXDC2 Gene

  • Plexin Domain Containing 2 2 3 5
  • Tumor Endothelial Marker 7-Related Protein 3 4
  • Plexin Domain-Containing Protein 2 3 4
  • TEM7R 3 4
  • Tumor Endothelial Marker 7-Related Precursor 2
  • 1200007L24Rik 3

External Ids for PLXDC2 Gene

Previous GeneCards Identifiers for PLXDC2 Gene

  • GC10P020255
  • GC10P020109
  • GC10P020145

Summaries for PLXDC2 Gene

GeneCards Summary for PLXDC2 Gene

PLXDC2 (Plexin Domain Containing 2) is a Protein Coding gene. Diseases associated with PLXDC2 include Vulva Cancer and Vulva Squamous Cell Carcinoma. An important paralog of this gene is PLXDC1.

UniProtKB/Swiss-Prot Summary for PLXDC2 Gene

Gene Wiki entry for PLXDC2 Gene

Additional gene information for PLXDC2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLXDC2 Gene

Genomics for PLXDC2 Gene

GeneHancer (GH) Regulatory Elements for PLXDC2 Gene

Promoters and enhancers for PLXDC2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J019814 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 +1.5 1474 5.8 EP300 CTCF ZFX ZIC2 ZBTB26 SAP30 RAD21 TRIM22 SMC3 HDAC2 ENSG00000285852 PLXDC2 ENSG00000233968 MALRD1 RF00017-608
GH10J020002 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 30.2 +188.3 188265 3.5 SIN3A SP1 FOS EP300 MEF2C RCOR1 TRIM22 FOXA2 BCL11A NR2F2 PLXDC2 ENSG00000238246 piR-32214-040 piR-31937-020
GH10J019944 Enhancer 0.9 Ensembl ENCODE dbSUPER 16.2 +130.3 130274 3.4 EP300 TCF12 ZNF384 MEF2B NR2F2 EBF1 IKZF1 NR2F1 TBX21 ZNF217 PLXDC2 ENSG00000238246 piR-31937-020 piR-32214-040
GH10J019960 Enhancer 1 FANTOM5 Ensembl dbSUPER 15.2 +144.2 144174 6 EP300 SRF NBN IKZF1 TBP RAD21 TBX21 ZNF687 MTA2 IKZF2 PLXDC2 ENSG00000238246 piR-31937-020 piR-32214-040
GH10J019774 Enhancer 0.7 FANTOM5 Ensembl ENCODE 19.1 -41.3 -41326 4.2 NFE2 POLR2A PLXDC2 MALRD1 ENSG00000233968 ENSG00000200545 lnc-NEBL-3 RNU6-1212P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLXDC2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PLXDC2

Top Transcription factor binding sites by QIAGEN in the PLXDC2 gene promoter:
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1a
  • NF-1
  • NF-1/L
  • Nkx2-5
  • oct-B2
  • oct-B3
  • POU2F2 (Oct-2.1)

Genomic Locations for PLXDC2 Gene

Genomic Locations for PLXDC2 Gene
chr10:19,816,227-20,289,856
(GRCh38/hg38)
Size:
473,630 bases
Orientation:
Plus strand
chr10:20,105,168-20,578,785
(GRCh37/hg19)
Size:
473,618 bases
Orientation:
Plus strand

Genomic View for PLXDC2 Gene

Genes around PLXDC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXDC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXDC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXDC2 Gene

Proteins for PLXDC2 Gene

  • Protein details for PLXDC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UX71-PXDC2_HUMAN
    Recommended name:
    Plexin domain-containing protein 2
    Protein Accession:
    Q6UX71
    Secondary Accessions:
    • Q96E59
    • Q96PD9
    • Q96SU9

    Protein attributes for PLXDC2 Gene

    Size:
    529 amino acids
    Molecular mass:
    59583 Da
    Quaternary structure:
    • Interacts with CTTN.

    Alternative splice isoforms for PLXDC2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLXDC2 Gene

Post-translational modifications for PLXDC2 Gene

  • Glycosylation at Ser86, Asn103, Asn160, Asn316, and Asn345
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PXDC2_HUMAN (1616)

Other Protein References for PLXDC2 Gene

No data available for DME Specific Peptides for PLXDC2 Gene

Domains & Families for PLXDC2 Gene

Gene Families for PLXDC2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PLXDC2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PLXDC2 Gene

GenScript: Design optimal peptide antigens:
  • Tumor endothelial marker 7-related protein (PXDC2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6UX71

UniProtKB/Swiss-Prot:

PXDC2_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXDC2: view

Function for PLXDC2 Gene

Molecular function for PLXDC2 Gene

UniProtKB/Swiss-Prot Function:
May play a role in tumor angiogenesis.

Phenotypes From GWAS Catalog for PLXDC2 Gene

Gene Ontology (GO) - Molecular Function for PLXDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15574754
genes like me logo Genes that share ontologies with PLXDC2: view
genes like me logo Genes that share phenotypes with PLXDC2: view

Animal Models for PLXDC2 Gene

MGI Knock Outs for PLXDC2:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLXDC2

CRISPR Products

miRNA for PLXDC2 Gene

miRTarBase miRNAs that target PLXDC2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXDC2 Gene

Localization for PLXDC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXDC2 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PLXDC2 gene
Compartment Confidence
plasma membrane 3
extracellular 2
cytosol 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PLXDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PLXDC2: view

Pathways & Interactions for PLXDC2 Gene

PathCards logo

SuperPathways for PLXDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PLXDC2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PLXDC2 Gene

Drugs & Compounds for PLXDC2 Gene

No Compound Related Data Available

Transcripts for PLXDC2 Gene

mRNA/cDNA for PLXDC2 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLXDC2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1:
SP2: -

Relevant External Links for PLXDC2 Gene

GeneLoc Exon Structure for
PLXDC2

Expression for PLXDC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLXDC2 Gene

Protein differential expression in normal tissues from HIPED for PLXDC2 Gene

This gene is overexpressed in Serum (23.3) and Vitreous humor (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PLXDC2 Gene



Protein tissue co-expression partners for PLXDC2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PLXDC2

SOURCE GeneReport for Unigene cluster for PLXDC2 Gene:

Hs.658134

mRNA Expression by UniProt/SwissProt for PLXDC2 Gene:

Q6UX71-PXDC2_HUMAN
Tissue specificity: Expressed in the endothelial cells of the stroma but not in the endothelial cells of normal colonic tissue.

Evidence on tissue expression from TISSUES for PLXDC2 Gene

  • Blood(4.2)
  • Bone marrow(4.1)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with PLXDC2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXDC2 Gene

Orthologs for PLXDC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLXDC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLXDC2 31 30
  • 99.43 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PLXDC2 31 30
  • 91.49 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLXDC2 31 30
  • 89.73 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Plxdc2 17 31 30
  • 87.31 (n)
rat
(Rattus norvegicus)
Mammalia Plxdc2 30
  • 87.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PLXDC2 31
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PLXDC2 31
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLXDC2 31 30
  • 79.36 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLXDC2 31
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plxdc2 30
  • 73.56 (n)
zebrafish
(Danio rerio)
Actinopterygii plxdc2 30
  • 68.86 (n)
ZPLXDC2 31
  • 64 (a)
OneToMany
PLXDC2 (2 of 2) 31
  • 48 (a)
OneToMany
wufb39a09 30
fruit fly
(Drosophila melanogaster)
Insecta l(1)G0289 31 30
  • 52.38 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004689 30
  • 50.42 (n)
worm
(Caenorhabditis elegans)
Secernentea pxd-1 31 30
  • 49.36 (n)
OneToMany
Species where no ortholog for PLXDC2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PLXDC2 Gene

ENSEMBL:
Gene Tree for PLXDC2 (if available)
TreeFam:
Gene Tree for PLXDC2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLXDC2: view image

Paralogs for PLXDC2 Gene

Paralogs for PLXDC2 Gene

(1) SIMAP similar genes for PLXDC2 Gene using alignment to 1 proteins:

  • PXDC2_HUMAN
genes like me logo Genes that share paralogs with PLXDC2: view

Variants for PLXDC2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PLXDC2 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs2778979 - p.Ile458Val
rs3817405 - p.Val396Ile

Additional dbSNP identifiers (rs#s) for PLXDC2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PLXDC2 Gene

Variant ID Type Subtype PubMed ID
dgv131n67 CNV loss 20364138
dgv191e212 CNV loss 25503493
dgv376n106 CNV deletion 24896259
dgv377n106 CNV deletion 24896259
dgv70n27 CNV loss 19166990
dgv988n54 CNV loss 21841781
dgv989n54 CNV loss 21841781
esv1408727 CNV insertion 17803354
esv1437455 CNV insertion 17803354
esv1569434 CNV insertion 17803354
esv2447411 CNV deletion 19546169
esv2657012 CNV deletion 23128226
esv2662651 CNV deletion 23128226
esv2667086 CNV deletion 23128226
esv2676030 CNV deletion 23128226
esv2733918 CNV deletion 23290073
esv2733929 CNV deletion 23290073
esv2759738 CNV gain+loss 17122850
esv3304544 CNV mobile element insertion 20981092
esv3306399 CNV mobile element insertion 20981092
esv3308968 CNV mobile element insertion 20981092
esv3324414 CNV insertion 20981092
esv3333698 CNV insertion 20981092
esv3355353 CNV insertion 20981092
esv3418941 CNV insertion 20981092
esv34306 CNV loss 17911159
esv34798 CNV loss 17911159
esv35130 CNV loss 17911159
esv3546000 CNV deletion 23714750
esv3578707 CNV loss 25503493
esv3578708 CNV loss 25503493
esv3622550 CNV loss 21293372
esv3622553 CNV loss 21293372
esv3622554 CNV loss 21293372
esv3891773 CNV loss 25118596
nsv1035861 CNV loss 25217958
nsv1049295 CNV loss 25217958
nsv1052454 CNV loss 25217958
nsv1113257 CNV deletion 24896259
nsv1116634 CNV tandem duplication 24896259
nsv1119786 CNV deletion 24896259
nsv1132839 CNV insertion 24896259
nsv1150554 CNV insertion 26484159
nsv24525 CNV insertion 16902084
nsv437096 CNV loss 16327808
nsv438165 CNV loss 16468122
nsv510213 OTHER sequence alteration 20534489
nsv520788 CNV loss 19592680
nsv550141 CNV loss 21841781
nsv820086 CNV gain 19587683
nsv825277 CNV loss 20364138
nsv947762 CNV duplication 23825009
nsv957543 CNV deletion 24416366
nsv957600 CNV deletion 24416366

Variation tolerance for PLXDC2 Gene

Residual Variation Intolerance Score: 28.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXDC2 Gene

Human Gene Mutation Database (HGMD)
PLXDC2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXDC2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXDC2 Gene

Disorders for PLXDC2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PLXDC2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
vulva cancer
  • ca vulva
vulva squamous cell carcinoma
  • squamous cell carcinoma of vulva
glaucoma, normal tension
  • glaucoma, normal tension, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXDC2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PLXDC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXDC2 Gene

Publications for PLXDC2 Gene

  1. Cell surface tumor endothelial markers are conserved in mice and humans. (PMID: 11559528) Carson-Walter EB … St Croix B (Cancer research 2001) 2 3 4 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population. (PMID: 19625618) Nakano M … Tashiro K (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 41 54
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 41 54
  5. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T … Smith RD (Journal of proteome research 2005) 3 4 54

Products for PLXDC2 Gene

Sources for PLXDC2 Gene