Plxnb1 plexin B1 [Rattus norvegicus (Norway rat)] - Gene

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, Dec 2024]
Expression: Biased expression in Heart (RPKM 163.4), Adrenal (RPKM 112.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Increased BMSC exosomal miR-140-3p alleviates bone degradation and promotes bone restoration by targeting Plxnb1 in diabetic rats.
Title: Increased BMSC exosomal miR-140-3p alleviates bone degradation and promotes bone restoration by targeting Plxnb1 in diabetic rats.
These results demonstrate a novel physiological function for sema4D/plxnB1 signaling in retinal pigment epithelium phagocytosis.
Title: Semaphorin4D-PlexinB1 Signaling Attenuates Photoreceptor Outer Segment Phagocytosis by Reducing Rac1 Activity of RPE Cells.
Skeletal fluorosis in vitro is caused by inhibition of osteogenesis via Sema4D/Plexin-B1 signaling pathway.
Title: Role of inhibition of osteogenesis function by Sema4D/Plexin-B1 signaling pathway in skeletal fluorosis in vitro.
p190 transiently associates with plexins, and its RhoGAP activity is increased in response to semaphorin stimulation. We conclude that p190-RhoGAP is crucially involved in semaphorin signalling to the actin cytoskeleton, via interaction with plexins.
Title: p190 Rho-GTPase activating protein associates with plexins and it is required for semaphorin signalling.
Plexin-B1 mediates Sema4D-induced repulsive axon guidance signaling by acting as a GTPase activating protein for R-Ras.
Title: The Semaphorin 4D receptor Plexin-B1 is a GTPase activating protein for R-Ras.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI112406 (e-PCR)
- UniSTS:245534

Plxnb1 (e-PCR), detects polymorphism
- UniSTS:546955

BF411491 (e-PCR)
- UniSTS:247706

BE110100 (e-PCR)
- UniSTS:245189

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

General protein information

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Preferred Names: plexin-B1

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)

NM_001108188.2 → NP_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:641 → 677

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:669 → 824

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:1068 → 1159

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:481 → 533

PSI; Plexin repeat

pfam08337
Location:1548 → 2088

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:541 → 627

TIG_plexin; TIG domain

pfam18020
Location:919 → 1018

TIG_2; TIG domain found in plexin

cl15674
Location:1250 → 1362

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:28 → 480

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

NC_086026.1 Reference GRCr8

Range

118621961..118647491

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006243883.5 → XP_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:641 → 677

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:669 → 824

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:1068 → 1159

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:481 → 533

PSI; Plexin repeat

pfam08337
Location:1548 → 2088

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:541 → 627

TIG_plexin; TIG domain

pfam18020
Location:919 → 1018

TIG_2; TIG domain found in plexin

cl15674
Location:1250 → 1362

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:28 → 480

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006243885.5 → XP_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:641 → 677

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:669 → 824

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:1068 → 1159

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:481 → 533

PSI; Plexin repeat

pfam08337
Location:1548 → 2088

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:541 → 627

TIG_plexin; TIG domain

pfam18020
Location:919 → 1018

TIG_2; TIG domain found in plexin

cl15674
Location:1250 → 1362

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:28 → 480

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039081605.2 → XP_038937533.1 plexin-B1 isoform X2

Related

ENSRNOP00000100942.1, ENSRNOT00000172966.1

Conserved Domains (9) summary

smart00423
Location:484 → 520

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:512 → 667

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:911 → 1002

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:324 → 376

PSI; Plexin repeat

pfam08337
Location:1391 → 1931

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:384 → 470

TIG_plexin; TIG domain

pfam18020
Location:762 → 861

TIG_2; TIG domain found in plexin

cl15674
Location:1093 → 1205

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:45 → 323

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039081604.2 → XP_038937532.1 plexin-B1 isoform X1

UniProtKB/TrEMBL

D3ZDX5

Conserved Domains (9) summary

smart00423
Location:641 → 677

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:669 → 824

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:1068 → 1159

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:481 → 533

PSI; Plexin repeat

pfam08337
Location:1548 → 2088

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:541 → 627

TIG_plexin; TIG domain

pfam18020
Location:919 → 1018

TIG_2; TIG domain found in plexin

cl15674
Location:1250 → 1362

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:28 → 480

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006243884.5 → XP_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:641 → 677

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:669 → 824

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:1068 → 1159

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:481 → 533

PSI; Plexin repeat

pfam08337
Location:1548 → 2088

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:541 → 627

TIG_plexin; TIG domain

pfam18020
Location:919 → 1018

TIG_2; TIG domain found in plexin

cl15674
Location:1250 → 1362

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:28 → 480

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039081606.2 → XP_038937534.1 plexin-B1 isoform X3

Conserved Domains (6) summary

smart00423
Location:12 → 48

PSI; domain found in Plexins, Semaphorins and Integrins

PHA03247
Location:40 → 195

PHA03247; large tegument protein UL36; Provisional

cd01180
Location:439 → 530

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:919 → 1459

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam18020
Location:290 → 389

TIG_2; TIG domain found in plexin

cl15674
Location:621 → 733

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 ...