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    PLXND1 plexin D1 [ Homo sapiens (human) ]

    Gene ID: 23129, updated on 11-Apr-2024

    Summary

    Official Symbol
    PLXND1provided by HGNC
    Official Full Name
    plexin D1provided by HGNC
    Primary source
    HGNC:HGNC:9107
    See related
    Ensembl:ENSG00000004399 MIM:604282; AllianceGenome:HGNC:9107
    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
    CHTD9; PLEXD1
    Summary
    Enables protein domain specific binding activity. Predicted to be involved in several processes, including endothelial cell migration; nervous system development; and regulation of angiogenesis. Predicted to act upstream of or within several processes, including circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and positive regulation of protein binding activity. Located in lamellipodium. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta (RPKM 37.7), fat (RPKM 32.1) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PLXND1 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129555214..129606676, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132299641..132351112, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129274057..129325519, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129247433-129248158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129248159-129248884 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129253999-129254668 Neighboring gene rhodopsin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129261557-129262058 Neighboring gene Sharpr-MPRA regulatory region 2951 Neighboring gene H1.8 linker histone Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129277154-129278043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129291899-129292624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129295530-129296256 Neighboring gene RNA, 7SL, cytoplasmic 752, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129315061-129315792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129321778-129322770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129323763-129324755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129325748-129326740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129326741-129327731 Neighboring gene uncharacterized LOC124909431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129330613-129331535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129331536-129332457 Neighboring gene Sharpr-MPRA regulatory region 12201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129342361-129343136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129343789-129344398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20518 Neighboring gene CARMIL2 pseudogene 1

    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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0620, MGC75353

    Gene Ontology Provided by GOA

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_015103.3NP_055918.3  plexin-D1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC023162, AC080007
      Consensus CDS
      CCDS33854.1
      UniProtKB/Swiss-Prot
      A7E2C6, C9JPZ6, Q6PJS9, Q8IZJ2, Q9BTQ2, Q9Y4D7
      Related
      ENSP00000317128.4, ENST00000324093.9
      Conserved Domains (8) 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
      pfam17960
      Location:627700
      TIG_plexin; TIG domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      129555214..129606676 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512589.2XP_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_011512588.3XP_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 X6

      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_047447765.1XP_047303721.1  plexin-D1 isoform X3

    5. XM_011512590.3XP_011510892.1  plexin-D1 isoform X4

      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
    6. XM_047447766.1XP_047303722.1  plexin-D1 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      132299641..132351112 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345793.1XP_054201768.1  plexin-D1 isoform X2

    2. XM_054345792.1XP_054201767.1  plexin-D1 isoform X1

    3. XM_054345797.1XP_054201772.1  plexin-D1 isoform X6

    4. XM_054345794.1XP_054201769.1  plexin-D1 isoform X3

    5. XM_054345795.1XP_054201770.1  plexin-D1 isoform X4

    6. XM_054345796.1XP_054201771.1  plexin-D1 isoform X5