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Plxnb1 plexin B1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 316009, updated on 27-Nov-2024

Summary

Symbol
Plxnb1provided by RGD
Full Name
plexin B1provided by RGD
Primary source
RGD:1310564
See related
EnsemblRapid:ENSRNOG00000029510 AllianceGenome:RGD:1310564
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable GTPase activating protein binding activity and semaphorin receptor activity. Predicted to be involved in several processes, including negative regulation of osteoblast proliferation; nervous system development; and positive regulation of intracellular signal transduction. Is active in glutamatergic synapse and postsynaptic membrane. Orthologous to human PLXNB1 (plexin B1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Heart (RPKM 163.4), Adrenal (RPKM 112.2) and 9 other tissues See more
Orthologs
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Genomic context

See Plxnb1 in Genome Data Viewer
Location:
8q32
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (118621961..118647491)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (109743470..109769153)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (117832826..117858515)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene U2 spliceosomal RNA Neighboring gene coiled-coil domain containing 51 Neighboring gene translation machinery associated 7 homolog Neighboring gene cytochrome c oxidase subunit 6C, pseudogene 2 Neighboring gene F-box and WD repeat domain containing 12 Neighboring gene serine peptidase inhibitor, Kazal type 8

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables GTPase activating protein binding ISO
Inferred from Sequence Orthology
more info
 
enables semaphorin receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables semaphorin receptor activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in inhibitory synapse assembly ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of osteoblast proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in neuron projection morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in ossification involved in bone maturation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of GTPase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of Rho protein signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within positive regulation of axonogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of cell shape IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of cell shape ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in semaphorin-plexin signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in postsynaptic membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of semaphorin receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of semaphorin receptor complex ISO
Inferred from Sequence Orthology
more info
 

NCBI Reference Sequences (RefSeq)

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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_001108188.2NP_001101658.2  plexin-B1 precursor

    Status: VALIDATED

    Source sequence(s)
    CA504175, JAXUCZ010000008
    UniProtKB/TrEMBL
    D3ZDX5
    Related
    ENSRNOP00000048230.3, ENSRNOT00000043345.7
    Conserved Domains (9) summary
    smart00423
    Location:641677
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:669824
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:10681159
    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 ...
    pfam01437
    Location:481533
    PSI; Plexin repeat
    pfam08337
    Location:15482088
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:541627
    TIG_plexin; TIG domain
    pfam18020
    Location:9191018
    TIG_2; TIG domain found in plexin
    cl15674
    Location:12501362
    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 ...
    cl15693
    Location:28480
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    118621961..118647491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006243883.5XP_006243945.1  plexin-B1 isoform X1

    See identical proteins and their annotated locations for XP_006243945.1

    UniProtKB/TrEMBL
    D3ZDX5
    Conserved Domains (9) summary
    smart00423
    Location:641677
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:669824
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:10681159
    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 ...
    pfam01437
    Location:481533
    PSI; Plexin repeat
    pfam08337
    Location:15482088
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:541627
    TIG_plexin; TIG domain
    pfam18020
    Location:9191018
    TIG_2; TIG domain found in plexin
    cl15674
    Location:12501362
    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 ...
    cl15693
    Location:28480
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. XM_006243885.5XP_006243947.1  plexin-B1 isoform X1

    See identical proteins and their annotated locations for XP_006243947.1

    UniProtKB/TrEMBL
    D3ZDX5
    Conserved Domains (9) summary
    smart00423
    Location:641677
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:669824
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:10681159
    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 ...
    pfam01437
    Location:481533
    PSI; Plexin repeat
    pfam08337
    Location:15482088
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:541627
    TIG_plexin; TIG domain
    pfam18020
    Location:9191018
    TIG_2; TIG domain found in plexin
    cl15674
    Location:12501362
    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 ...
    cl15693
    Location:28480
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  3. XM_039081605.2XP_038937533.1  plexin-B1 isoform X2

    Related
    ENSRNOP00000100942.1, ENSRNOT00000172966.1
    Conserved Domains (9) summary
    smart00423
    Location:484520
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:512667
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:9111002
    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 ...
    pfam01437
    Location:324376
    PSI; Plexin repeat
    pfam08337
    Location:13911931
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:384470
    TIG_plexin; TIG domain
    pfam18020
    Location:762861
    TIG_2; TIG domain found in plexin
    cl15674
    Location:10931205
    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 ...
    cl15693
    Location:45323
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_039081604.2XP_038937532.1  plexin-B1 isoform X1

    UniProtKB/TrEMBL
    D3ZDX5
    Conserved Domains (9) summary
    smart00423
    Location:641677
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:669824
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:10681159
    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 ...
    pfam01437
    Location:481533
    PSI; Plexin repeat
    pfam08337
    Location:15482088
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:541627
    TIG_plexin; TIG domain
    pfam18020
    Location:9191018
    TIG_2; TIG domain found in plexin
    cl15674
    Location:12501362
    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 ...
    cl15693
    Location:28480
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. XM_006243884.5XP_006243946.1  plexin-B1 isoform X1

    See identical proteins and their annotated locations for XP_006243946.1

    UniProtKB/TrEMBL
    D3ZDX5
    Conserved Domains (9) summary
    smart00423
    Location:641677
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:669824
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:10681159
    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 ...
    pfam01437
    Location:481533
    PSI; Plexin repeat
    pfam08337
    Location:15482088
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam17960
    Location:541627
    TIG_plexin; TIG domain
    pfam18020
    Location:9191018
    TIG_2; TIG domain found in plexin
    cl15674
    Location:12501362
    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 ...
    cl15693
    Location:28480
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. XM_039081606.2XP_038937534.1  plexin-B1 isoform X3

    Conserved Domains (6) summary
    smart00423
    Location:1248
    PSI; domain found in Plexins, Semaphorins and Integrins
    PHA03247
    Location:40195
    PHA03247; large tegument protein UL36; Provisional
    cd01180
    Location:439530
    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 ...
    pfam08337
    Location:9191459
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    pfam18020
    Location:290389
    TIG_2; TIG domain found in plexin
    cl15674
    Location:621733
    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 ...