Human Gene PLXND1 (ENST00000324093.9) from GENCODE V44
  Description: Homo sapiens plexin D1 (PLXND1), mRNA. (from RefSeq NM_015103)
Gencode Transcript: ENST00000324093.9
Gencode Gene: ENSG00000004399.13
Transcript (Including UTRs)
   Position: hg38 chr3:129,555,214-129,606,676 Size: 51,463 Total Exon Count: 36 Strand: -
Coding Region
   Position: hg38 chr3:129,556,312-129,606,639 Size: 50,328 Coding Exon Count: 36 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:129,555,214-129,606,676)mRNA (may differ from genome)Protein (1925 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLXD1_HUMAN
DESCRIPTION: RecName: Full=Plexin-D1; Flags: Precursor;
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.
SUBUNIT: Interacts with NRP1, SEMA4A, SEMA3A, SEMA3C and SEMA3E (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein (By similarity).
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.
SIMILARITY: Belongs to the plexin family.
SIMILARITY: Contains 3 IPT/TIG domains.
SIMILARITY: Contains 1 Sema domain.
SEQUENCE CAUTION: Sequence=BAA31595.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PLXND1
Diseases sorted by gene-association score: moebius syndrome* (370), conotruncal heart malformations* (132), ischemic retinopathy (17), endometrioid ovary carcinoma (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.81 RPKM in Lung
Total median expression: 805.99 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -11.5037-0.311 Picture PostScript Text
3' UTR -449.201098-0.409 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013783 - Ig-like_fold
IPR014756 - Ig_E-set
IPR002909 - IPT_TIG_rcpt
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR013548 - Plexin_cytoplasmic_RasGAP_dom
IPR002165 - Plexin_repeat
IPR008936 - Rho_GTPase_activation_prot
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF08337 - Plexin cytoplasmic RasGAP domain
PF01437 - Plexin repeat
PF01403 - Sema domain
PF01833 - IPT/TIG domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3H6N - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y4D7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017154 semaphorin receptor activity
GO:0019904 protein domain specific binding

Biological Process:
GO:0001525 angiogenesis
GO:0001569 branching involved in blood vessel morphogenesis
GO:0003151 outflow tract morphogenesis
GO:0003279 cardiac septum development
GO:0007162 negative regulation of cell adhesion
GO:0007165 signal transduction
GO:0007221 positive regulation of transcription of Notch receptor target
GO:0007275 multicellular organism development
GO:0007416 synapse assembly
GO:0008360 regulation of cell shape
GO:0030334 regulation of cell migration
GO:0032092 positive regulation of protein binding
GO:0035904 aorta development
GO:0043087 regulation of GTPase activity
GO:0043542 endothelial cell migration
GO:0045765 regulation of angiogenesis
GO:0050772 positive regulation of axonogenesis
GO:0060666 dichotomous subdivision of terminal units involved in salivary gland branching
GO:0060976 coronary vasculature development
GO:0071526 semaphorin-plexin signaling pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030027 lamellipodium
GO:0031258 lamellipodium membrane
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AY116661 - Homo sapiens plexin D1 (PLXND1) mRNA, complete cds.
BC062465 - Homo sapiens plexin D1, mRNA (cDNA clone IMAGE:6178111), complete cds.
BC044228 - Homo sapiens, Similar to plexin A, clone IMAGE:5211086, mRNA, partial cds.
BC030110 - Homo sapiens plexin D1, mRNA (cDNA clone IMAGE:4798761).
BC011848 - Homo sapiens plexin D1, mRNA (cDNA clone IMAGE:4121608), complete cds.
BC003526 - Homo sapiens, clone IMAGE:3607457, mRNA, partial cds.
JD411450 - Sequence 392474 from Patent EP1572962.
JD064195 - Sequence 45219 from Patent EP1572962.
JD088012 - Sequence 69036 from Patent EP1572962.
JD339163 - Sequence 320187 from Patent EP1572962.
AK026388 - Homo sapiens cDNA: FLJ22735 fis, clone HUV00180.
BC150280 - Homo sapiens plexin D1, mRNA (cDNA clone MGC:166893 IMAGE:9007263), complete cds.
AB014520 - Homo sapiens KIAA0620 mRNA for KIAA0620 protein.
JD143396 - Sequence 124420 from Patent EP1572962.
JD335848 - Sequence 316872 from Patent EP1572962.
JD072116 - Sequence 53140 from Patent EP1572962.
JD278586 - Sequence 259610 from Patent EP1572962.
JD086579 - Sequence 67603 from Patent EP1572962.
JD557604 - Sequence 538628 from Patent EP1572962.
JD104307 - Sequence 85331 from Patent EP1572962.
JD383565 - Sequence 364589 from Patent EP1572962.
JD075874 - Sequence 56898 from Patent EP1572962.
JD126201 - Sequence 107225 from Patent EP1572962.
AK299425 - Homo sapiens cDNA FLJ58111 complete cds, highly similar to Plexin-D1 precursor.
JD124162 - Sequence 105186 from Patent EP1572962.
JD270406 - Sequence 251430 from Patent EP1572962.
JD107780 - Sequence 88804 from Patent EP1572962.
JD126985 - Sequence 108009 from Patent EP1572962.
JD103495 - Sequence 84519 from Patent EP1572962.
JD411735 - Sequence 392759 from Patent EP1572962.
AB383924 - Synthetic construct DNA, clone: pF1KSDA0620, Homo sapiens PLXND1 gene for plexin-D1 precursor, complete cds, without stop codon, in Flexi system.
JD241152 - Sequence 222176 from Patent EP1572962.
JD054344 - Sequence 35368 from Patent EP1572962.
JD103176 - Sequence 84200 from Patent EP1572962.
JD044210 - Sequence 25234 from Patent EP1572962.
JD020676 - Sequence 1700 from Patent EP1572962.
JD030371 - Sequence 11395 from Patent EP1572962.
JD122713 - Sequence 103737 from Patent EP1572962.
JD142374 - Sequence 123398 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y4D7 (Reactome details) participates in the following event(s):

R-HSA-416683 SEMA3E binds to PLXND1
R-HSA-416690 SEMA4A binds to PLXND1
R-HSA-416700 Other semaphorin interactions
R-HSA-9013508 NOTCH3 Intracellular Domain Regulates Transcription
R-HSA-373755 Semaphorin interactions
R-HSA-9012852 Signaling by NOTCH3
R-HSA-422475 Axon guidance
R-HSA-157118 Signaling by NOTCH
R-HSA-1266738 Developmental Biology
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A7E2C6, C9JPZ6, ENST00000324093.1, ENST00000324093.2, ENST00000324093.3, ENST00000324093.4, ENST00000324093.5, ENST00000324093.6, ENST00000324093.7, ENST00000324093.8, KIAA0620, NM_015103, PLXD1_HUMAN, Q6PJS9, Q8IZJ2, Q9BTQ2, Q9Y4D7, uc003emx.1, uc003emx.2, uc003emx.3, uc003emx.4
UCSC ID: ENST00000324093.9
RefSeq Accession: NM_015103
Protein: Q9Y4D7 (aka PLXD1_HUMAN or PXD1_HUMAN)
CCDS: CCDS33854.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.