Human Gene PLXNB1 (uc003csw.2)
  Description: Homo sapiens plexin B1 (PLXNB1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:48,445,261-48,470,872 Size: 25,612 Total Exon Count: 38 Strand: -
Coding Region
   Position: hg19 chr3:48,445,893-48,466,020 Size: 20,128 Coding Exon Count: 36 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:48,445,261-48,470,872)mRNA (may differ from genome)Protein (2135 aa)
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neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLXB1_HUMAN
DESCRIPTION: RecName: Full=Plexin-B1; AltName: Full=Semaphorin receptor SEP; Flags: Precursor;
FUNCTION: Receptor for SEMA4D. Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration.
SUBUNIT: Monomer, and heterodimer with PLXNB2 after proteolytic processing. Binds RAC1 that has been activated by GTP binding. Interaction with SEMA4D promotes binding of cytoplasmic ligands. Binds PLXNA1 (By similarity). Interacts with ARHGEF11, ARHGEF12, ERBB2, MET, MST1R, RRAS, RHOD, RND1, NRP1 and NRP2.
INTERACTION: P08581:MET; NbExp=7; IntAct=EBI-1111488, EBI-1039152; Q04912:MST1R; NbExp=3; IntAct=EBI-1111488, EBI-2637518;
SUBCELLULAR LOCATION: Isoform 1: Cell membrane; Single-pass type I membrane protein.
SUBCELLULAR LOCATION: Isoform 2: Secreted.
SUBCELLULAR LOCATION: Isoform 3: Secreted.
TISSUE SPECIFICITY: Highly expressed in fetal kidney, and at slightly lower levels in fetal brain, lung and liver.
PTM: Phosphorylated on tyrosine residues by ERBB2 and MET upon SEMA4D binding.
PTM: Proteolytic processing favors heterodimerization with PLXNB2 and SEMA4D binding.
SIMILARITY: Belongs to the plexin family.
SIMILARITY: Contains 3 IPT/TIG domains.
SIMILARITY: Contains 1 Sema domain.
SEQUENCE CAUTION: Sequence=BAA23703.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PLXNB1
CDC HuGE Published Literature: PLXNB1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 63.91 RPKM in Thyroid
Total median expression: 1403.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -150.20270-0.556 Picture PostScript Text
3' UTR -279.00632-0.441 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015716 - CD2_adhesion_molc
IPR013783 - Ig-like_fold
IPR014756 - Ig_E-set
IPR002909 - IPT_TIG_rcpt
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR013548 - Plexin_cytoplasmic_RasGAP_dom
IPR002165 - Plexin_repeat
IPR001936 - RasGAP
IPR008936 - Rho_GTPase_activation_prot
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF01403 - Sema domain
PF01437 - Plexin repeat
PF01833 - IPT/TIG domain
PF08337 - Plexin cytoplasmic RasGAP domain

SCOP Domains:
48350 - GTPase activation domain, GAP
81296 - E set domains
101912 - Sema domain
103575 - Plexin repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JPH - NMR MuPIT 2OS6 - NMR MuPIT 2R2O - X-ray MuPIT 2REX - X-ray MuPIT 3HM6 - X-ray MuPIT 3OL2 - X-ray MuPIT 3SU8 - X-ray MuPIT 3SUA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43157
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0017154 semaphorin receptor activity
GO:0030215 semaphorin receptor binding
GO:0032794 GTPase activating protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0007162 negative regulation of cell adhesion
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0008360 regulation of cell shape
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling
GO:0016477 cell migration
GO:0033689 negative regulation of osteoblast proliferation
GO:0035556 intracellular signal transduction
GO:0043087 regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
GO:0043931 ossification involved in bone maturation
GO:0048675 axon extension
GO:0048812 neuron projection morphogenesis
GO:0050772 positive regulation of axonogenesis
GO:0051493 regulation of cytoskeleton organization
GO:0071526 semaphorin-plexin signaling pathway
GO:1900220 semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis

Cellular Component:
GO:0002116 semaphorin receptor complex
GO:0005576 extracellular region
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF208645 - JP 2014500723-A/16148: Polycomb-Associated Non-Coding RNAs.
JA482211 - Sequence 194 from Patent WO2011072091.
JE980503 - Sequence 194 from Patent EP2862929.
JA482212 - Sequence 195 from Patent WO2011072091.
JE980504 - Sequence 195 from Patent EP2862929.
AK126476 - Homo sapiens cDNA FLJ44512 fis, clone UTERU3001988, highly similar to Homo sapiens coatomer protein complex, subunit epsilon (COPE), transcript variant 2, mRNA.
AK091832 - Homo sapiens cDNA FLJ34513 fis, clone HLUNG2006582, highly similar to Plexin-B1 precursor.
AK092609 - Homo sapiens cDNA FLJ35290 fis, clone PROST2008271, highly similar to Plexin-B1 precursor.
AB007867 - Homo sapiens KIAA0407 mRNA.
BC146793 - Homo sapiens plexin B1, mRNA (cDNA clone MGC:166894 IMAGE:9007264), complete cds.
BC066773 - Homo sapiens cDNA clone IMAGE:30347721, containing frame-shift errors.
LF378667 - JP 2014500723-A/186170: Polycomb-Associated Non-Coding RNAs.
X87904 - Homo sapiens mRNA for semaphorin receptor (plexin-B1/SEP gene).
JD225737 - Sequence 206761 from Patent EP1572962.
JD219346 - Sequence 200370 from Patent EP1572962.
LF378666 - JP 2014500723-A/186169: Polycomb-Associated Non-Coding RNAs.
JD192746 - Sequence 173770 from Patent EP1572962.
JD496436 - Sequence 477460 from Patent EP1572962.
JD174407 - Sequence 155431 from Patent EP1572962.
JD160543 - Sequence 141567 from Patent EP1572962.
JD483233 - Sequence 464257 from Patent EP1572962.
LF378665 - JP 2014500723-A/186168: Polycomb-Associated Non-Coding RNAs.
JD277810 - Sequence 258834 from Patent EP1572962.
JD401167 - Sequence 382191 from Patent EP1572962.
JD194256 - Sequence 175280 from Patent EP1572962.
JD400247 - Sequence 381271 from Patent EP1572962.
JD116606 - Sequence 97630 from Patent EP1572962.
AK296776 - Homo sapiens cDNA FLJ57524 complete cds, highly similar to Plexin-B1 precursor.
AJ011415 - Homo sapiens mRNA for plexin-B1 plasma membrane receptor, splice variant R (plexin-B1/SEP gene).
AB384476 - Synthetic construct DNA, clone: pF1KA0407, Homo sapiens PLXNB1 gene for plexin-B1 precursor, complete cds, without stop codon, in Flexi system.
LF378664 - JP 2014500723-A/186167: Polycomb-Associated Non-Coding RNAs.
LF378663 - JP 2014500723-A/186166: Polycomb-Associated Non-Coding RNAs.
LN626690 - Homo sapiens partial mRNA for plexin B1 (PLXNB1 gene).
LF378661 - JP 2014500723-A/186164: Polycomb-Associated Non-Coding RNAs.
LF378660 - JP 2014500723-A/186163: Polycomb-Associated Non-Coding RNAs.
BC128094 - Homo sapiens plexin B1, mRNA (cDNA clone IMAGE:40109090), complete cds.
AJ011414 - Homo sapiens mRNA for plexin-B1 plasma membrane receptor, truncated splice variant (plexin-B1/SEP gene).
KJ901642 - Synthetic construct Homo sapiens clone ccsbBroadEn_11036 PLXNB1 gene, encodes complete protein.
BC129947 - Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10, mRNA (cDNA clone IMAGE:40124318), with apparent retained intron.
LF378658 - JP 2014500723-A/186161: Polycomb-Associated Non-Coding RNAs.
LF378656 - JP 2014500723-A/186159: Polycomb-Associated Non-Coding RNAs.
LF208644 - JP 2014500723-A/16147: Polycomb-Associated Non-Coding RNAs.
MA444222 - JP 2018138019-A/16148: Polycomb-Associated Non-Coding RNAs.
MA614244 - JP 2018138019-A/186170: Polycomb-Associated Non-Coding RNAs.
MA614243 - JP 2018138019-A/186169: Polycomb-Associated Non-Coding RNAs.
MA614242 - JP 2018138019-A/186168: Polycomb-Associated Non-Coding RNAs.
MA614241 - JP 2018138019-A/186167: Polycomb-Associated Non-Coding RNAs.
MA614240 - JP 2018138019-A/186166: Polycomb-Associated Non-Coding RNAs.
MA614238 - JP 2018138019-A/186164: Polycomb-Associated Non-Coding RNAs.
MA614237 - JP 2018138019-A/186163: Polycomb-Associated Non-Coding RNAs.
MA633497 - JP 2018521062-A/3: B1SP FUSION PROTEIN THERAPEUTICS, METHODS, AND USES.
MA614235 - JP 2018138019-A/186161: Polycomb-Associated Non-Coding RNAs.
MA614233 - JP 2018138019-A/186159: Polycomb-Associated Non-Coding RNAs.
MA444221 - JP 2018138019-A/16147: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

Reactome (by CSHL, EBI, and GO)

Protein O43157 (Reactome details) participates in the following event(s):

R-HSA-398185 LARG binds plexin B1
R-HSA-373750 SEMA4D interacts with Plexin-B1:ErbB2
R-HSA-419646 SEMA4D interacts with Plexin-B1:Met
R-HSA-400677 Rnd1 interacts with Plexin-B1:Sema4D
R-HSA-400682 Active Rac1 interacts with Plexin-B1:Sema4D
R-HSA-416562 p190RhoGAP binds Plexin-B1
R-HSA-416594 LARG and PDZ-RhoGEF binds to Plexin-B1
R-HSA-416546 Inactivation of R-Ras by Sema4D-Plexin-B1 GAP activity
R-HSA-416559 Inactivation of Rho-GTP by p190RhoGAP
R-HSA-416588 Activation of Rho by LARG and PDZ-RhoGEF
R-HSA-416482 G alpha (12/13) signalling events
R-HSA-416572 Sema4D induced cell migration and growth-cone collapse
R-HSA-416550 Sema4D mediated inhibition of cell attachment and migration
R-HSA-388396 GPCR downstream signalling
R-HSA-400685 Sema4D in semaphorin signaling
R-HSA-372790 Signaling by GPCR
R-HSA-373755 Semaphorin interactions
R-HSA-162582 Signal Transduction
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A6H8Y2, KIAA0407, NM_002673, NP_002664, O43157, PLXB1_HUMAN, PLXN5, Q6NY20, Q9UIV7, Q9UJ92, Q9UJ93, SEP
UCSC ID: uc003csw.2
RefSeq Accession: NM_002673
Protein: O43157 (aka PLXB1_HUMAN or PXB1_HUMAN)
CCDS: CCDS2765.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002673.4
exon count: 38CDS single in 3' UTR: no RNA size: 7325
ORF size: 6408CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 12747.00frame shift in genome: no % Coverage: 99.80
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.