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    PLXND1 plexin D1 [ Homo sapiens (human) ]

    Gene ID: 23129, updated on 12-May-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 current GRCh38.p12 (GCF_000001405.38) 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 RNA, 7SL, cytoplasmic 752, pseudogene Neighboring gene transmembrane and coiled-coil domain family 1 Neighboring gene RNY3 pseudogene 13 Neighboring gene TMCC1 antisense RNA 1 (head to head)

    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.p12 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p12 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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