Human Gene PLXNB2 (uc003bkv.4) Description and Page Index
  Description: Homo sapiens plexin B2 (PLXNB2), mRNA.
RefSeq Summary (NM_012401): Members of the B class of plexins, such as PLXNB2 are transmembrane receptors that participate in axon guidance and cell migration in response to semaphorins (Perrot et al. (2002) [PubMed 12183458]).[supplied by OMIM, Mar 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660805.70948.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000359337.9/ ENSP00000352288.4 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr22:50,713,408-50,746,001 Size: 32,594 Total Exon Count: 37 Strand: -
Coding Region
   Position: hg19 chr22:50,714,133-50,729,013 Size: 14,881 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:50,713,408-50,746,001)mRNA (may differ from genome)Protein (1838 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PLXB2_HUMAN
DESCRIPTION: RecName: Full=Plexin-B2; AltName: Full=MM1; Flags: Precursor;
FUNCTION: Cell surface receptor for SEMA4C, SEMA4D and SEMA4G that plays an important role in cell-cell signaling. Binding to class 4 semaphorins promotes downstream activation of RHOA and phosphorylation of ERBB2 at 'Tyr-1248'. Required for normal differentiation and migration of neuronal cells during brain corticogenesis and for normal embryonic brain development. Regulates the migration of cerebellar granule cells in the developing brain. Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. May modulate the activity of RAC1 and CDC42. Down-regulates macrophage migration in wound- healing assays (in vitro) (By similarity).
SUBUNIT: Monomer, and heterodimer with PLXNB1. Interacts with SEMA4C, SEMA4D and SEMA4G (By similarity). Binds MET, ARHGEF11 and ARHGEF12. May also interact with MST1R.
INTERACTION: P08581:MET; NbExp=2; IntAct=EBI-722004, EBI-1039152; Q04912:MST1R; NbExp=2; IntAct=EBI-722004, EBI-2637518;
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
SIMILARITY: Belongs to the plexin family.
SIMILARITY: Contains 3 IPT/TIG domains.
SIMILARITY: Contains 1 Sema domain.
SEQUENCE CAUTION: Sequence=BAA21571.1; Type=Erroneous initiation;

-  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: 88.13 RPKM in Brain - Cerebellum
Total median expression: 1980.21 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 -27.6093-0.297 Picture PostScript Text
3' UTR -306.30725-0.422 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
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

4E71
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O15031
FrontTopSide
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
      
      
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017154 semaphorin receptor activity

Biological Process:
GO:0001843 neural tube closure
GO:0001932 regulation of protein phosphorylation
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007162 negative regulation of cell adhesion
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0007405 neuroblast proliferation
GO:0007420 brain development
GO:0008360 regulation of cell shape
GO:0010976 positive regulation of neuron projection development
GO:0043087 regulation of GTPase activity
GO:0050772 positive regulation of axonogenesis
GO:0071526 semaphorin-plexin signaling pathway
GO:2001222 regulation of neuron migration

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF210401 - JP 2014500723-A/17904: Polycomb-Associated Non-Coding RNAs.
BC000221 - Homo sapiens plexin B2, mRNA (cDNA clone IMAGE:3352923), **** WARNING: chimeric clone ****.
AB002313 - Homo sapiens mRNA for KIAA0315 gene.
BC127770 - Homo sapiens plexin B2, mRNA (cDNA clone IMAGE:40128271), complete cds.
AB383845 - Synthetic construct DNA, clone: pF1KSDA0315, Homo sapiens PLXNB2 gene for plexin-B2 precursor, complete cds, without stop codon, in Flexi system.
BC172440 - Synthetic construct Homo sapiens clone IMAGE:100069134, MGC:199145 plexin B2 (PLXNB2) mRNA, encodes complete protein.
MA445978 - JP 2018138019-A/17904: Polycomb-Associated Non-Coding RNAs.
BC110366 - Homo sapiens plexin B2, mRNA (cDNA clone IMAGE:5403399), partial cds.
AK123131 - Homo sapiens cDNA FLJ41136 fis, clone BRACE2029112, moderately similar to Homo sapiens mRNA for plexin-B1 plasma membrane receptor.
AK025415 - Homo sapiens cDNA: FLJ21762 fis, clone COLF6920.
AK074932 - Homo sapiens cDNA FLJ90451 fis, clone NT2RP3001416, highly similar to Plexin B2.
AK056543 - Homo sapiens cDNA FLJ31981 fis, clone NT2RP7008543, weakly similar to PLEXIN 4 PRECURSOR.
AB075511 - Homo sapiens neuroblastoma cDNA, clone:Nbla00445, full insert sequence.
AK025701 - Homo sapiens cDNA: FLJ22048 fis, clone HEP09323.
BC004542 - Homo sapiens plexin B2, mRNA (cDNA clone IMAGE:3951420), partial cds.
BC067216 - Homo sapiens cDNA clone IMAGE:6187057, **** WARNING: chimeric clone ****.
AK126394 - Homo sapiens cDNA FLJ44430 fis, clone UTERU2017762, moderately similar to Homo sapiens plexin B1 (PLXNB1).
JD483898 - Sequence 464922 from Patent EP1572962.
JD222520 - Sequence 203544 from Patent EP1572962.
JD176208 - Sequence 157232 from Patent EP1572962.
JD138367 - Sequence 119391 from Patent EP1572962.
JD216638 - Sequence 197662 from Patent EP1572962.
JD451627 - Sequence 432651 from Patent EP1572962.
JD056972 - Sequence 37996 from Patent EP1572962.
JD383117 - Sequence 364141 from Patent EP1572962.
JD383116 - Sequence 364140 from Patent EP1572962.
LF337584 - JP 2014500723-A/145087: Polycomb-Associated Non-Coding RNAs.
JD117467 - Sequence 98491 from Patent EP1572962.
JD479497 - Sequence 460521 from Patent EP1572962.
JD533623 - Sequence 514647 from Patent EP1572962.
JD440266 - Sequence 421290 from Patent EP1572962.
BT006887 - Homo sapiens plexin B2 mRNA, complete cds.
LF337585 - JP 2014500723-A/145088: Polycomb-Associated Non-Coding RNAs.
LF337586 - JP 2014500723-A/145089: Polycomb-Associated Non-Coding RNAs.
LF337587 - JP 2014500723-A/145090: Polycomb-Associated Non-Coding RNAs.
S76730 - MM1=clone MM1 product [human, fetal brain, mRNA Partial, 1396 nt].
LF337588 - JP 2014500723-A/145091: Polycomb-Associated Non-Coding RNAs.
LF337589 - JP 2014500723-A/145092: Polycomb-Associated Non-Coding RNAs.
BC148225 - Homo sapiens cDNA clone IMAGE:40085345.
BC148280 - Homo sapiens cDNA clone IMAGE:40085346.
LF337590 - JP 2014500723-A/145093: Polycomb-Associated Non-Coding RNAs.
LF337591 - JP 2014500723-A/145094: Polycomb-Associated Non-Coding RNAs.
LF337592 - JP 2014500723-A/145095: Polycomb-Associated Non-Coding RNAs.
LF337593 - JP 2014500723-A/145096: Polycomb-Associated Non-Coding RNAs.
LF337594 - JP 2014500723-A/145097: Polycomb-Associated Non-Coding RNAs.
LF337595 - JP 2014500723-A/145098: Polycomb-Associated Non-Coding RNAs.
LF337596 - JP 2014500723-A/145099: Polycomb-Associated Non-Coding RNAs.
LF337597 - JP 2014500723-A/145100: Polycomb-Associated Non-Coding RNAs.
LF337598 - JP 2014500723-A/145101: Polycomb-Associated Non-Coding RNAs.
LF337599 - JP 2014500723-A/145102: Polycomb-Associated Non-Coding RNAs.
LF337600 - JP 2014500723-A/145103: Polycomb-Associated Non-Coding RNAs.
DQ589406 - Homo sapiens piRNA piR-56518, complete sequence.
LF337601 - JP 2014500723-A/145104: Polycomb-Associated Non-Coding RNAs.
LF337602 - JP 2014500723-A/145105: Polycomb-Associated Non-Coding RNAs.
LF337603 - JP 2014500723-A/145106: Polycomb-Associated Non-Coding RNAs.
LF337604 - JP 2014500723-A/145107: Polycomb-Associated Non-Coding RNAs.
LF337605 - JP 2014500723-A/145108: Polycomb-Associated Non-Coding RNAs.
LF337606 - JP 2014500723-A/145109: Polycomb-Associated Non-Coding RNAs.
LF337607 - JP 2014500723-A/145110: Polycomb-Associated Non-Coding RNAs.
LF337608 - JP 2014500723-A/145111: Polycomb-Associated Non-Coding RNAs.
LF337609 - JP 2014500723-A/145112: Polycomb-Associated Non-Coding RNAs.
LF337610 - JP 2014500723-A/145113: Polycomb-Associated Non-Coding RNAs.
LF337611 - JP 2014500723-A/145114: Polycomb-Associated Non-Coding RNAs.
MA573161 - JP 2018138019-A/145087: Polycomb-Associated Non-Coding RNAs.
MA573162 - JP 2018138019-A/145088: Polycomb-Associated Non-Coding RNAs.
MA573163 - JP 2018138019-A/145089: Polycomb-Associated Non-Coding RNAs.
MA573164 - JP 2018138019-A/145090: Polycomb-Associated Non-Coding RNAs.
MA573165 - JP 2018138019-A/145091: Polycomb-Associated Non-Coding RNAs.
MA573166 - JP 2018138019-A/145092: Polycomb-Associated Non-Coding RNAs.
MA573167 - JP 2018138019-A/145093: Polycomb-Associated Non-Coding RNAs.
MA573168 - JP 2018138019-A/145094: Polycomb-Associated Non-Coding RNAs.
MA573169 - JP 2018138019-A/145095: Polycomb-Associated Non-Coding RNAs.
MA573170 - JP 2018138019-A/145096: Polycomb-Associated Non-Coding RNAs.
MA573171 - JP 2018138019-A/145097: Polycomb-Associated Non-Coding RNAs.
MA573172 - JP 2018138019-A/145098: Polycomb-Associated Non-Coding RNAs.
MA573173 - JP 2018138019-A/145099: Polycomb-Associated Non-Coding RNAs.
MA573174 - JP 2018138019-A/145100: Polycomb-Associated Non-Coding RNAs.
MA573175 - JP 2018138019-A/145101: Polycomb-Associated Non-Coding RNAs.
MA573176 - JP 2018138019-A/145102: Polycomb-Associated Non-Coding RNAs.
MA573177 - JP 2018138019-A/145103: Polycomb-Associated Non-Coding RNAs.
MA573178 - JP 2018138019-A/145104: Polycomb-Associated Non-Coding RNAs.
MA573179 - JP 2018138019-A/145105: Polycomb-Associated Non-Coding RNAs.
MA573180 - JP 2018138019-A/145106: Polycomb-Associated Non-Coding RNAs.
MA573181 - JP 2018138019-A/145107: Polycomb-Associated Non-Coding RNAs.
MA573182 - JP 2018138019-A/145108: Polycomb-Associated Non-Coding RNAs.
MA573183 - JP 2018138019-A/145109: Polycomb-Associated Non-Coding RNAs.
MA573184 - JP 2018138019-A/145110: Polycomb-Associated Non-Coding RNAs.
MA573185 - JP 2018138019-A/145111: Polycomb-Associated Non-Coding RNAs.
MA573186 - JP 2018138019-A/145112: Polycomb-Associated Non-Coding RNAs.
MA573187 - JP 2018138019-A/145113: Polycomb-Associated Non-Coding RNAs.
MA573188 - JP 2018138019-A/145114: Polycomb-Associated Non-Coding RNAs.
LF337612 - JP 2014500723-A/145115: Polycomb-Associated Non-Coding RNAs.
LF337613 - JP 2014500723-A/145116: Polycomb-Associated Non-Coding RNAs.
LF337614 - JP 2014500723-A/145117: Polycomb-Associated Non-Coding RNAs.
LF337615 - JP 2014500723-A/145118: Polycomb-Associated Non-Coding RNAs.
LF337616 - JP 2014500723-A/145119: Polycomb-Associated Non-Coding RNAs.
LF337617 - JP 2014500723-A/145120: Polycomb-Associated Non-Coding RNAs.
LF337618 - JP 2014500723-A/145121: Polycomb-Associated Non-Coding RNAs.
LF337619 - JP 2014500723-A/145122: Polycomb-Associated Non-Coding RNAs.
LF337620 - JP 2014500723-A/145123: Polycomb-Associated Non-Coding RNAs.
LF337621 - JP 2014500723-A/145124: Polycomb-Associated Non-Coding RNAs.
LF337622 - JP 2014500723-A/145125: Polycomb-Associated Non-Coding RNAs.
LF337626 - JP 2014500723-A/145129: Polycomb-Associated Non-Coding RNAs.
MA573189 - JP 2018138019-A/145115: Polycomb-Associated Non-Coding RNAs.
MA573190 - JP 2018138019-A/145116: Polycomb-Associated Non-Coding RNAs.
MA573191 - JP 2018138019-A/145117: Polycomb-Associated Non-Coding RNAs.
MA573192 - JP 2018138019-A/145118: Polycomb-Associated Non-Coding RNAs.
MA573193 - JP 2018138019-A/145119: Polycomb-Associated Non-Coding RNAs.
MA573194 - JP 2018138019-A/145120: Polycomb-Associated Non-Coding RNAs.
MA573195 - JP 2018138019-A/145121: Polycomb-Associated Non-Coding RNAs.
MA573196 - JP 2018138019-A/145122: Polycomb-Associated Non-Coding RNAs.
MA573197 - JP 2018138019-A/145123: Polycomb-Associated Non-Coding RNAs.
MA573198 - JP 2018138019-A/145124: Polycomb-Associated Non-Coding RNAs.
MA573199 - JP 2018138019-A/145125: Polycomb-Associated Non-Coding RNAs.
MA573203 - JP 2018138019-A/145129: Polycomb-Associated Non-Coding RNAs.

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

-  Other Names for This Gene
  Alternate Gene Symbols: A6QRH0, KIAA0315, NM_012401, NP_036533, O15031, PLXB2_HUMAN, Q7KZU3, Q9BSU7
UCSC ID: uc003bkv.4
RefSeq Accession: NM_012401
Protein: O15031 (aka PLXB2_HUMAN or PXB2_HUMAN)
CCDS: CCDS43035.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012401.3
exon count: 37CDS single in 3' UTR: no RNA size: 6356
ORF size: 5517CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 11123.00frame shift in genome: no % Coverage: 99.67
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.