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Aliases for PLXND1 Gene

Aliases for PLXND1 Gene

  • Plexin D1 2 3 5
  • Plexin-D1 3
  • KIAA0620 4
  • PLEXD1 3

External Ids for PLXND1 Gene

Previous GeneCards Identifiers for PLXND1 Gene

  • GC03U990121
  • GC03M129910
  • GC03M130555
  • GC03M130594
  • GC03M130756
  • GC03M129274
  • GC03M126657

Summaries for PLXND1 Gene

GeneCards Summary for PLXND1 Gene

PLXND1 (Plexin D1) is a Protein Coding gene. Diseases associated with PLXND1 include Moebius Syndrome and Conotruncal Heart Malformations. Among its related pathways are Semaphorin interactions and Developmental Biology. Gene Ontology (GO) annotations related to this gene include receptor activity and semaphorin receptor activity. An important paralog of this gene is PLXNB1.

UniProtKB/Swiss-Prot for PLXND1 Gene

  • Cell surface receptor for SEMA4A and for class 3 semaphorins, such as SEMA3A, SEMA3C and SEMA3E. Plays an important role in cell-cell signaling, and in regulating the migration of a wide spectrum of cell types. Regulates the migration of thymocytes in the medulla. Regulates endothelial cell migration. Plays an important role in ensuring the specificity of synapse formation. Required for normal development of the heart and vasculature (By similarity). Mediates anti-angiogenic signaling in response to SEMA3E.

Gene Wiki entry for PLXND1 Gene

Additional gene information for PLXND1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLXND1 Gene

Genomics for PLXND1 Gene

GeneHancer (GH) Regulatory Elements for PLXND1 Gene

Promoters and enhancers for PLXND1 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
GH03I129591 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 558.5 +5.8 5844 19.4 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A YBX1 FEZF1 DMAP1 PLXND1 RPL32P3 IFT122 LINC02021 ACAD9 H1FX-AS1 RHO ENSG00000244932 ENSG00000203644 H1FOO
GH03I129489 Enhancer 1.3 Ensembl ENCODE dbSUPER 24.4 +115.8 115791 2.9 PKNOX1 MLX ZFP64 ARID4B ZNF2 ZNF48 ARID2 ZNF207 ZNF143 FOS PIR61564 PLXND1 RPL32P3 IFT122 RHO RNY3P13 MBD4 PIR46036
GH03I129438 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.2 +166.1 166096 4.5 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B IFT122 MBD4 RPL32P3 PLXND1 RHO GC03P129766 GC03P129770 PIR50923
GH03I129493 Enhancer 1.1 Ensembl ENCODE dbSUPER 24.8 +111.6 111636 3.3 FOXA2 JUN CTBP1 GATA3 LCORL ATF7 FOS TCF7L2 RFX1 ZNF687 PLXND1 IFT122 RHO RNY3P13 MBD4 PIR61564 PIR46036
GH03I129533 Enhancer 0.8 ENCODE 21.8 +72.1 72126 1.4 RARA ATF7 EGR2 SP5 CEBPB ZFP69B IKZF1 CEBPA HNF4A ZBTB26 PLXND1 RPL32P3 IFT122 MBD4 H1FOO RHO
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PLXND1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLXND1 gene promoter:

Genomic Locations for PLXND1 Gene

Genomic Locations for PLXND1 Gene
chr3:129,555,175-129,606,818
(GRCh38/hg38)
Size:
51,644 bases
Orientation:
Minus strand
chr3:129,274,018-129,325,661
(GRCh37/hg19)

Genomic View for PLXND1 Gene

Genes around PLXND1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXND1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXND1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXND1 Gene

Proteins for PLXND1 Gene

  • Protein details for PLXND1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4D7-PLXD1_HUMAN
    Recommended name:
    Plexin-D1
    Protein Accession:
    Q9Y4D7
    Secondary Accessions:
    • A7E2C6
    • C9JPZ6
    • Q6PJS9
    • Q8IZJ2
    • Q9BTQ2

    Protein attributes for PLXND1 Gene

    Size:
    1925 amino acids
    Molecular mass:
    212007 Da
    Quaternary structure:
    • Interacts with NRP1 and SEMA4A (By similarity). Interacts with SH3BP1; they dissociate upon SEMA3E binding to PLXND1 allowing SH3BP1 to transduce downstream signal through RAC1 inactivation (PubMed:24841563).
    SequenceCaution:
    • Sequence=BAA31595.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLXND1 Gene

    Alternative splice isoforms for PLXND1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLXND1 Gene

Post-translational modifications for PLXND1 Gene

  • Glycosylation at Asn86, Asn155, Asn188, isoforms=2224, isoforms=2481, Asn500, Asn583, isoforms=2696, isoforms=2736, Asn802, Asn965, Asn1017, Asn1060, Asn1099, isoforms=21118, Asn1132, isoforms=21237, and isoforms=21257

No data available for DME Specific Peptides for PLXND1 Gene

Domains & Families for PLXND1 Gene

Gene Families for PLXND1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for PLXND1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y4D7

UniProtKB/Swiss-Prot:

PLXD1_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXND1: view

Function for PLXND1 Gene

Molecular function for PLXND1 Gene

GENATLAS Biochemistry:
plexin D1,calcium-dependent cell adhesion molecule at the neuronal cell surface,receptor for the semaphorin 7A (SEMA7A)
UniProtKB/Swiss-Prot Function:
Cell surface receptor for SEMA4A and for class 3 semaphorins, such as SEMA3A, SEMA3C and SEMA3E. Plays an important role in cell-cell signaling, and in regulating the migration of a wide spectrum of cell types. Regulates the migration of thymocytes in the medulla. Regulates endothelial cell migration. Plays an important role in ensuring the specificity of synapse formation. Required for normal development of the heart and vasculature (By similarity). Mediates anti-angiogenic signaling in response to SEMA3E.

Phenotypes From GWAS Catalog for PLXND1 Gene

Gene Ontology (GO) - Molecular Function for PLXND1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17318185
GO:0017154 semaphorin receptor activity ISS,IEA --
GO:0019904 protein domain specific binding IPI 24841563
genes like me logo Genes that share ontologies with PLXND1: view
genes like me logo Genes that share phenotypes with PLXND1: view

Human Phenotype Ontology for PLXND1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLXND1 Gene

MGI Knock Outs for PLXND1:

Animal Model Products

CRISPR Products

miRNA for PLXND1 Gene

miRTarBase miRNAs that target PLXND1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PLXND1 Gene

Localization for PLXND1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXND1 Gene

Cell membrane; Single-pass membrane protein. Cell projection, lamellipodium membrane.

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 PLXND1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PLXND1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane ISS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030027 lamellipodium IDA 24841563
genes like me logo Genes that share ontologies with PLXND1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLXND1 Gene

Pathways & Interactions for PLXND1 Gene

genes like me logo Genes that share pathways with PLXND1: view

Pathways by source for PLXND1 Gene

Gene Ontology (GO) - Biological Process for PLXND1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis ISS --
GO:0001569 branching involved in blood vessel morphogenesis IEA --
GO:0003151 outflow tract morphogenesis IEA --
GO:0003279 cardiac septum development IEA --
GO:0007162 negative regulation of cell adhesion IBA --
genes like me logo Genes that share ontologies with PLXND1: view

No data available for SIGNOR curated interactions for PLXND1 Gene

Drugs & Compounds for PLXND1 Gene

No Compound Related Data Available

Transcripts for PLXND1 Gene

Unigene Clusters for PLXND1 Gene

Plexin D1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLXND1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ^ 11a · 11b ^ 12a · 12b · 12c · 12d ^ 13a · 13b ^ 14a · 14b ·
SP1:
SP2:
SP3: - - - - - - -
SP4: - -
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10: -
SP11: -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18: -
SP19:
SP20:
SP21:

ExUns: 14c ^ 15a · 15b ^ 16 ^ 17 ^ 18a · 18b · 18c ^ 19a · 19b ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b · 23c · 23d ^ 24 ^ 25a · 25b ^ 26 ^ 27 ^ 28 ^ 29a · 29b ^
SP1: - -
SP2: -
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:

ExUns: 30 ^ 31a · 31b ^ 32a · 32b ^ 33 ^ 34a · 34b ^ 35a · 35b · 35c
SP1: - - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17: -
SP18:
SP19:
SP20:
SP21:

Relevant External Links for PLXND1 Gene

GeneLoc Exon Structure for
PLXND1
ECgene alternative splicing isoforms for
PLXND1

Expression for PLXND1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLXND1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLXND1 Gene

This gene is overexpressed in Serum (23.4), Breast (13.4), Stomach (12.8), and Heart (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLXND1 Gene



NURSA nuclear receptor signaling pathways regulating expression of PLXND1 Gene:

PLXND1

SOURCE GeneReport for Unigene cluster for PLXND1 Gene:

Hs.301685

mRNA Expression by UniProt/SwissProt for PLXND1 Gene:

Q9Y4D7-PLXD1_HUMAN
Tissue specificity: Detected at low levels in heart, placenta, lung, skeletal muscle, kidney, thymus and liver. Detected at very low levels in brain, colon, spleen, small intestine and peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for PLXND1 Gene

  • Nervous system(4.7)
  • Muscle(4.4)
  • Bone marrow(4.3)
  • Liver(4.3)
  • Heart(2.9)
  • Stomach(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXND1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • pituitary gland
  • skull
  • vocal cord
Thorax:
  • aorta
  • breast
  • chest wall
  • esophagus
  • heart
  • heart valve
  • lung
Abdomen:
  • stomach
Pelvis:
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
genes like me logo Genes that share expression patterns with PLXND1: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for PLXND1 Gene

Orthologs for PLXND1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLXND1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLXND1 34
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
OneToMany
-- 34
  • 70 (a)
OneToMany
dog
(Canis familiaris)
Mammalia PLXND1 34 33
  • 90.99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLXND1 33 34
  • 90.23 (n)
mouse
(Mus musculus)
Mammalia Plxnd1 33 16 34
  • 87.19 (n)
rat
(Rattus norvegicus)
Mammalia Plxnd1 33
  • 86.48 (n)
oppossum
(Monodelphis domestica)
Mammalia PLXND1 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLXND1 33 34
  • 74.86 (n)
lizard
(Anolis carolinensis)
Reptilia PLXND1 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plxnd1 33
  • 65.47 (n)
zebrafish
(Danio rerio)
Actinopterygii PLXND1 34
  • 90 (a)
OneToOne
plxnd1 33
  • 66.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta plexB 34
  • 28 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea plx-2 34
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToOne
Species where no ortholog for PLXND1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 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 PLXND1 Gene

ENSEMBL:
Gene Tree for PLXND1 (if available)
TreeFam:
Gene Tree for PLXND1 (if available)

Paralogs for PLXND1 Gene

Paralogs for PLXND1 Gene

genes like me logo Genes that share paralogs with PLXND1: view

Variants for PLXND1 Gene

Sequence variations from dbSNP and Humsavar for PLXND1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000034245 -- 129,570,496(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000078489 -- 129,575,866(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000095867 -- 129,581,131(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000142314 -- 129,607,773(-) A/G upstream_transcript_variant
rs1000183964 -- 129,595,320(-) G/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PLXND1 Gene

Variant ID Type Subtype PubMed ID
dgv4858n100 CNV gain 25217958
dgv4859n100 CNV gain 25217958
dgv8579n54 CNV loss 21841781
esv27314 CNV loss 19812545
nsv508953 CNV insertion 20534489
nsv519392 CNV gain 19592680
nsv520828 CNV loss 19592680
nsv522149 CNV loss 19592680
nsv591669 CNV loss 21841781
nsv591672 CNV gain 21841781
nsv591674 CNV loss 21841781
nsv591675 CNV loss 21841781
nsv955346 CNV deletion 24416366

Variation tolerance for PLXND1 Gene

Residual Variation Intolerance Score: 94.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.87; 89.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXND1 Gene

Human Gene Mutation Database (HGMD)
PLXND1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXND1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXND1 Gene

Disorders for PLXND1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PLXND1 Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
moebius syndrome
  • mbs
conotruncal heart malformations
  • cthm
ischemic retinopathy
endometrioid ovary carcinoma
  • endometrioid carcinoma of ovary
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXND1

genes like me logo Genes that share disorders with PLXND1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXND1 Gene

Publications for PLXND1 Gene

  1. PLEXIN-D1, a novel plexin family member, is expressed in vascular endothelium and the central nervous system during mouse embryogenesis. (PMID: 12412018) van der Zwaag B … Van Bokhoven H (Developmental dynamics : an official publication of the American Association of Anatomists 2002) 2 3 4 22 58
  2. Semaphorin 3E initiates antiangiogenic signaling through plexin D1 by regulating Arf6 and R-Ras. (PMID: 20385769) Sakurai A … Gutkind JS (Molecular and cellular biology 2010) 3 4 22 58
  3. An image-based RNAi screen identifies SH3BP1 as a key effector of Semaphorin 3E-PlexinD1 signaling. (PMID: 24841563) Tata A … Gu C (The Journal of cell biology 2014) 3 4 58
  4. Plexin D1 is ubiquitously expressed on tumor vessels and tumor cells in solid malignancies. (PMID: 19703316) Roodink I … Leenders WP (BMC cancer 2009) 3 22 58
  5. Semaphorin 3E expression correlates inversely with Plexin D1 during tumor progression. (PMID: 18974298) Roodink I … Leenders W (The American journal of pathology 2008) 3 22 58

Products for PLXND1 Gene

Sources for PLXND1 Gene

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