Plxnb3 (plexin B3) - Rat Genome Database

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Gene: Plxnb3 (plexin B3) Rattus norvegicus
Analyze
Symbol: Plxnb3
Name: plexin B3
RGD ID: 1560615
Description: Predicted to enable several functions, including Rho GDP-dissociation inhibitor binding activity; cell-cell adhesion mediator activity; and semaphorin receptor activity. Involved in negative regulation of cell migration; negative regulation of lamellipodium assembly; and semaphorin-plexin signaling pathway. Predicted to be located in cell surface. Predicted to be part of semaphorin receptor complex. Orthologous to human PLXNB3 (plexin B3); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC363517; plexin-B3; RGD1560615; similar to Plexin B3 precursor (Plexin 6)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,645,505 - 156,660,011 (+)NCBIGRCr8
mRatBN7.2X151,493,832 - 151,508,688 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,494,207 - 151,508,674 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,636,711 - 153,649,852 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,199,937 - 157,213,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,871,765 - 154,884,906 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,015,297 - 157,030,147 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,015,305 - 157,028,434 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,764,184 - 152,779,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,681,646 - 159,694,783 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1136,380,863 - 136,394,000 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Semaphorin 5A and plexin-B3 inhibit human glioma cell motility through RhoGDIalpha-mediated inactivation of Rac1 GTPase. Li X and Lee AY, J Biol Chem. 2010 Oct 15;285(42):32436-45. doi: 10.1074/jbc.M110.120451. Epub 2010 Aug 9.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15218527   PMID:16122393   PMID:18680721   PMID:19850054   PMID:25989221   PMID:34267322  


Genomics

Comparative Map Data
Plxnb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,645,505 - 156,660,011 (+)NCBIGRCr8
mRatBN7.2X151,493,832 - 151,508,688 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,494,207 - 151,508,674 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,636,711 - 153,649,852 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,199,937 - 157,213,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,871,765 - 154,884,906 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,015,297 - 157,030,147 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,015,305 - 157,028,434 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,764,184 - 152,779,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,681,646 - 159,694,783 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1136,380,863 - 136,394,000 (-)NCBICelera
Cytogenetic MapXq37NCBI
PLXNB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,764,249 - 153,779,341 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,764,196 - 153,779,346 (+)EnsemblGRCh38hg38GRCh38
GRCh37X153,029,704 - 153,044,796 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,682,905 - 152,697,989 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X152,550,557 - 152,565,642NCBI
CeleraX153,263,333 - 153,278,483 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,686,716 - 141,701,865 (+)NCBIHuRef
CHM1_1X152,904,061 - 152,919,212 (+)NCBICHM1_1
T2T-CHM13v2.0X152,037,914 - 152,053,006 (+)NCBIT2T-CHM13v2.0
Plxnb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,800,564 - 72,816,116 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,800,696 - 72,816,120 (+)EnsemblGRCm39 Ensembl
GRCm38X73,756,556 - 73,772,510 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,757,090 - 73,772,514 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X71,002,442 - 71,017,849 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X70,009,810 - 70,025,230 (+)NCBIMGSCv36mm8
CeleraX65,009,376 - 65,024,783 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.4NCBI
Plxnb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580484,805 - 495,445 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955580482,602 - 495,628 (+)NCBIChiLan1.0ChiLan1.0
PLXNB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,804,772 - 153,820,041 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,808,363 - 153,823,646 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,314,794 - 143,330,066 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,200,971 - 153,215,909 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,200,971 - 153,215,909 (+)Ensemblpanpan1.1panPan2
PLXNB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,577,564 - 121,593,294 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,580,073 - 121,593,287 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX106,906,928 - 106,922,587 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X124,719,222 - 124,734,893 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX124,719,296 - 124,734,838 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X120,488,510 - 120,504,170 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,003,521 - 123,019,170 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X122,765,705 - 122,781,365 (+)NCBIUU_Cfam_GSD_1.0
Plxnb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,905,069 - 118,921,958 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936809644,049 - 659,859 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936809645,569 - 659,850 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLXNB3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,509,526 - 124,522,767 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,507,953 - 124,522,780 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,072,571 - 142,087,361 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLXNB3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,191,297 - 128,207,456 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX128,191,332 - 128,206,194 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606566,058,633 - 66,073,613 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plxnb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946450,047 - 460,718 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624946447,981 - 460,880 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:71
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000056397
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
A008P20  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01152,767,470 - 152,767,951NCBIRnor5.0
RGSC_v3.4X159,691,016 - 159,691,496UniSTSRGSC3.4
Cytogenetic MapXq37UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 27 3
Low 2 16 2 2 2 19 23 2 2
Below cutoff 1 27 16 3 17 3 6 9 18 23 15 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000080088   ⟹   ENSRNOP00000072671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,494,207 - 151,508,674 (+)Ensembl
Rnor_6.0 EnsemblX157,015,305 - 157,028,434 (-)Ensembl
RefSeq Acc Id: NM_001135878   ⟹   NP_001129350
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,646,874 - 156,660,011 (+)NCBI
mRatBN7.2X151,495,545 - 151,508,682 (+)NCBI
Rnor_6.0X157,015,297 - 157,028,434 (-)NCBI
Rnor_5.01152,764,184 - 152,779,039 (-)NCBI
RGSC_v3.4X159,681,646 - 159,694,783 (+)RGD
Celera1136,380,863 - 136,394,000 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229587   ⟹   XP_006229649
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,507 - 156,660,011 (+)NCBI
mRatBN7.2X151,494,180 - 151,508,688 (+)NCBI
Rnor_6.0X157,015,297 - 157,029,849 (-)NCBI
Rnor_5.01152,764,184 - 152,779,039 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773631   ⟹   XP_008771853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,506 - 156,660,011 (+)NCBI
mRatBN7.2X151,493,832 - 151,508,688 (+)NCBI
Rnor_6.0X157,015,297 - 157,030,147 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773632   ⟹   XP_008771854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,506 - 156,660,011 (+)NCBI
mRatBN7.2X151,494,179 - 151,508,688 (+)NCBI
Rnor_6.0X157,015,297 - 157,029,850 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602116   ⟹   XP_017457605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,506 - 156,660,011 (+)NCBI
mRatBN7.2X151,494,179 - 151,508,688 (+)NCBI
Rnor_6.0X157,015,297 - 157,029,851 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099913   ⟹   XP_038955841
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,505 - 156,656,915 (+)NCBI
mRatBN7.2X151,494,177 - 151,505,588 (+)NCBI
RefSeq Acc Id: XM_063280161   ⟹   XP_063136231
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,645,507 - 156,660,011 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001129350   ⟸   NM_001135878
- Peptide Label: precursor
- UniProtKB: D3ZLH5 (UniProtKB/Swiss-Prot),   A6KRV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229649   ⟸   XM_006229587
- Peptide Label: isoform X2
- UniProtKB: D3ZLH5 (UniProtKB/Swiss-Prot),   A6KRV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771853   ⟸   XM_008773631
- Peptide Label: isoform X1
- UniProtKB: A6KRV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771854   ⟸   XM_008773632
- Peptide Label: isoform X3
- UniProtKB: A6KRV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457605   ⟸   XM_017602116
- Peptide Label: isoform X1
- UniProtKB: A6KRV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072671   ⟸   ENSRNOT00000080088
RefSeq Acc Id: XP_038955841   ⟸   XM_039099913
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063136231   ⟸   XM_063280161
- Peptide Label: isoform X4
Protein Domains
IPT/TIG   PSI   Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLH5-F1-model_v2 AlphaFold D3ZLH5 1-1902 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560615 AgrOrtholog
BioCyc Gene G2FUF-663 BioCyc
Ensembl Genes ENSRNOG00000061731 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055024415 UniProtKB/Swiss-Prot
  ENSRNOG00060006263 UniProtKB/Swiss-Prot
  ENSRNOG00065014631 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000080088.2 UniProtKB/Swiss-Prot
  ENSRNOT00055041966 UniProtKB/Swiss-Prot
  ENSRNOT00060010309 UniProtKB/Swiss-Prot
  ENSRNOT00065024205 UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  YVTN repeat-like/Quinoprotein amine dehydrogenase UniProtKB/TrEMBL
InterPro Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_E-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPT_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plexin_cytoplasmic_RasGAP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plexin_RBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plexin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rho_GTPase_activation_prot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIG1_plexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIG2_plexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363517 UniProtKB/Swiss-Prot
NCBI Gene 363517 ENTREZGENE
PANTHER PLEXIN UniProtKB/TrEMBL
  PLEXIN-B3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR22625 UniProtKB/Swiss-Prot
Pfam Plexin_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plexin_RBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIG_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIG_plexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Plxnb3 PhenoGen
PROSITE SEMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000061731 RatGTEx
  ENSRNOG00055024415 RatGTEx
  ENSRNOG00060006263 RatGTEx
  ENSRNOG00065014631 RatGTEx
SMART IPT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP E set domains UniProtKB/TrEMBL
  GTPase activation domain, GAP UniProtKB/TrEMBL
  Plexin repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema domain UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  SSF48350 UniProtKB/Swiss-Prot
  SSF81296 UniProtKB/Swiss-Prot
UniProt A6KRV8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLH5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Plxnb3  plexin B3   Plxnb3_predicted  plexin B3 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Plxnb3_predicted  plexin B3 (predicted)  RGD1560615_predicted  similar to Plexin B3 precursor (Plexin 6) (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1560615_predicted  similar to Plexin B3 precursor (Plexin 6) (predicted)  LOC363517  similar to Plexin B3 precursor (Plexin 6)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363517  similar to Plexin B3 precursor (Plexin 6)      Symbol and Name status set to provisional 70820 PROVISIONAL