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PLXND1 plexin D1 [ Homo sapiens (human) ]

Gene ID: 23129, updated on 17-Jun-2019

Summary

Official Symbol
PLXND1provided by HGNC
Official Full Name
plexin D1provided by HGNC
Primary source
HGNC:HGNC:9107
See related
Ensembl:ENSG00000004399 MIM:604282
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
PLEXD1
Expression
Broad expression in placenta (RPKM 37.7), fat (RPKM 32.1) and 23 other tissues See more
Orthologs

Genomic context

See PLXND1 in Genome Data Viewer
Location:
3q22.1
Exon count:
37
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (129555213..129606739, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129274056..129325582, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene rhodopsin Neighboring gene H1 histone family member O oocyte specific Neighboring gene Sharpr-MPRA regulatory region 1469 Neighboring gene RNA, 7SL, cytoplasmic 752, pseudogene Neighboring gene Sharpr-MPRA regulatory region 12201 Neighboring gene Sharpr-MPRA regulatory region 14456

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Other semaphorin interactions, organism-specific biosystem (from REACTOME)
    Other semaphorin interactions, organism-specific biosystemThere are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secre...
  • Semaphorin interactions, organism-specific biosystem (from REACTOME)
    Semaphorin interactions, organism-specific biosystemSemaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphor...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0620, MGC75353

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
semaphorin receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
aorta development IEA
Inferred from Electronic Annotation
more info
 
branching involved in blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cardiac septum development IEA
Inferred from Electronic Annotation
more info
 
coronary vasculature development IEA
Inferred from Electronic Annotation
more info
 
dichotomous subdivision of terminal units involved in salivary gland branching IEA
Inferred from Electronic Annotation
more info
 
endothelial cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endothelial cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
outflow tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription of Notch receptor target TAS
Traceable Author Statement
more info
 
regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell shape IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
semaphorin-plexin signaling pathway involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
semaphorin receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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_015103.2NP_055918.2  plexin-D1 precursor

    See identical proteins and their annotated locations for NP_055918.2

    Status: VALIDATED

    Source sequence(s)
    AC023162, AY116661, BC150280, BU527983, CX761094
    Consensus CDS
    CCDS33854.1
    UniProtKB/Swiss-Prot
    Q9Y4D7
    Related
    ENSP00000317128.4, ENST00000324093.8
    Conserved Domains (7) summary
    cd11247
    Location:49547
    Sema_plexin_D1; The Sema domain, a protein interacting module, of Plexin D1
    smart00423
    Location:711753
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd01179
    Location:9811067
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01180
    Location:891979
    IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:10691174
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam01437
    Location:549601
    PSI; Plexin repeat
    pfam08337
    Location:13451888
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    129555213..129606739 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512589.1XP_011510891.1  plexin-D1 isoform X2

    Conserved Domains (6) summary
    cd11247
    Location:49547
    Sema_plexin_D1; The Sema domain, a protein interacting module, of Plexin D1
    cd01179
    Location:851937
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01180
    Location:761849
    IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:9391044
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam01437
    Location:549601
    PSI; Plexin repeat
    pfam08337
    Location:12151758
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
  2. XM_011512588.2XP_011510890.1  plexin-D1 isoform X1

    Conserved Domains (7) summary
    cd11247
    Location:49547
    Sema_plexin_D1; The Sema domain, a protein interacting module, of Plexin D1
    smart00423
    Location:711753
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd01179
    Location:9811067
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01180
    Location:891979
    IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:10691174
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam01437
    Location:549601
    PSI; Plexin repeat
    pfam08337
    Location:13451887
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
  3. XM_011512592.1XP_011510894.1  plexin-D1 isoform X4

    Conserved Domains (4) summary
    cd01179
    Location:37123
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:125230
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam08337
    Location:401944
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    cl15674
    Location:335
    IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...
  4. XM_011512590.2XP_011510892.1  plexin-D1 isoform X3

    Conserved Domains (7) summary
    cd11247
    Location:49547
    Sema_plexin_D1; The Sema domain, a protein interacting module, of Plexin D1
    smart00423
    Location:711753
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd01179
    Location:9811067
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01180
    Location:891979
    IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:10691174
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam01437
    Location:549601
    PSI; Plexin repeat
    cl02569
    Location:13441439
    RasGAP; Ras GTPase Activating Domain

RNA

  1. XR_924116.1 RNA Sequence

  2. XR_001740063.1 RNA Sequence

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