Plxna3 (plexin A3) - Rat Genome Database

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Gene: Plxna3 (plexin A3) Rattus norvegicus
Analyze
Symbol: Plxna3
Name: plexin A3
RGD ID: 1584973
Description: Predicted to have semaphorin receptor activity. Predicted to be involved in several processes, including negative chemotaxis; nervous system development; and regulation of GTPase activity. Predicted to localize to integral component of plasma membrane and semaphorin receptor complex. Orthologous to human PLXNA3 (plexin A3); INTERACTS WITH 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Plexin 4; Plexin 4, SEX, homolog to the cMet/HGF receptors; plexin A3 (mapped); plexin-A3; Plxn4; Plxna3_mapped; SEX
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X152,115,699 - 152,131,608 (+)NCBI
Rnor_6.0 EnsemblX156,363,405 - 156,379,189 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X156,363,400 - 156,379,433 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,103,535 - 152,119,342 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,261,781 - 160,277,570 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1135,765,043 - 135,780,832 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:18804103   PMID:19717441   PMID:21835343   PMID:23063687  


Genomics

Comparative Map Data
Plxna3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X152,115,699 - 152,131,608 (+)NCBI
Rnor_6.0 EnsemblX156,363,405 - 156,379,189 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X156,363,400 - 156,379,433 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,103,535 - 152,119,342 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,261,781 - 160,277,570 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1135,765,043 - 135,780,832 (-)NCBICelera
Cytogenetic MapXq37NCBI
PLXNA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX154,458,281 - 154,477,779 (+)EnsemblGRCh38hg38GRCh38
GRCh38X154,458,281 - 154,477,779 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X153,686,621 - 153,706,118 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,339,817 - 153,355,179 (+)NCBINCBI36hg18NCBI36
Build 34X153,250,326 - 153,265,688NCBI
CeleraX153,847,674 - 153,863,036 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX142,263,786 - 142,279,038 (+)NCBIHuRef
CHM1_1X153,598,265 - 153,613,630 (+)NCBICHM1_1
Plxna3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,372,644 - 73,388,295 (+)NCBIGRCm39mm39
GRCm39 EnsemblX73,372,672 - 73,388,295 (+)Ensembl
GRCm38X74,328,290 - 74,344,689 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,329,066 - 74,344,689 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X71,574,405 - 71,590,028 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X70,581,819 - 70,596,483 (+)NCBImm8
CeleraX65,582,855 - 65,598,478 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX38.0NCBI
Plxna3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580957,860 - 972,772 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955580958,033 - 972,123 (+)NCBIChiLan1.0ChiLan1.0
PLXNA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X153,772,700 - 153,786,167 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,772,700 - 153,786,167 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X143,900,029 - 143,915,391 (+)NCBIMhudiblu_PPA_v0panPan3
PLXNA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,165,460 - 122,180,727 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX122,167,144 - 122,180,951 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X125,307,120 - 125,321,660 (+)NCBI
UMICH_Zoey_3.1X121,076,136 - 121,090,670 (+)NCBI
UNSW_CanFamBas_1.0X123,591,257 - 123,605,728 (+)NCBI
UU_Cfam_GSD_1.0X123,352,967 - 123,367,509 (+)NCBI
Plxna3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,471,987 - 119,488,955 (+)NCBI
SpeTri2.0NW_0049368091,209,787 - 1,226,726 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLXNA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,984,190 - 124,997,067 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,982,307 - 124,997,098 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X143,588,358 - 143,603,211 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLXNA3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,706,354 - 128,721,971 (+)NCBI
ChlSab1.1 EnsemblX128,708,424 - 128,721,971 (+)Ensembl
Plxna3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624946924,956 - 939,483 (+)NCBI

Position Markers
RH131167  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,130,726 - 152,130,908 (-)MAPPER
Rnor_6.0X156,364,100 - 156,364,281NCBIRnor6.0
Rnor_5.01152,104,235 - 152,104,416UniSTSRnor5.0
RGSC_v3.4X160,262,481 - 160,262,662UniSTSRGSC3.4
Celera1135,765,743 - 135,765,924UniSTS
Cytogenetic MapXq37UniSTS
REN89674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,120,474 - 152,120,806 (-)MAPPER
Rnor_6.0X156,374,202 - 156,374,533NCBIRnor6.0
Rnor_5.01152,114,336 - 152,114,667UniSTSRnor5.0
RGSC_v3.4X160,272,583 - 160,272,914UniSTSRGSC3.4
Celera1135,775,845 - 135,776,176UniSTS
Cytogenetic MapXq37UniSTS
REN89678  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X152,121,515 - 152,121,792 (-)MAPPER
Rnor_6.0X156,373,216 - 156,373,492NCBIRnor6.0
Rnor_5.01152,113,350 - 152,113,626UniSTSRnor5.0
RGSC_v3.4X160,271,597 - 160,271,873UniSTSRGSC3.4
Celera1135,774,859 - 135,775,135UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X134627816159970021Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:825
Count of miRNA genes:296
Interacting mature miRNAs:375
Transcripts:ENSRNOT00000056307
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


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 8 4 4 4 68 14 28
Low 3 35 48 32 19 32 8 11 6 21 11 11 8
Below cutoff 5 5 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083148   ⟹   ENSRNOP00000068735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX156,363,405 - 156,379,189 (-)Ensembl
RefSeq Acc Id: NM_001107581   ⟹   NP_001101051
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X152,115,819 - 152,131,608 (+)NCBI
Rnor_6.0X156,363,400 - 156,379,189 (-)NCBI
Rnor_5.01152,103,535 - 152,119,342 (-)NCBI
RGSC_v3.4X160,261,781 - 160,277,570 (-)RGD
Celera1135,765,043 - 135,780,832 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229577   ⟹   XP_006229639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X152,115,699 - 152,131,164 (+)NCBI
Rnor_6.0X156,363,400 - 156,379,334 (-)NCBI
Rnor_5.01152,103,535 - 152,119,342 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773598   ⟹   XP_008771820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X156,363,400 - 156,379,035 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773599   ⟹   XP_008771821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X152,115,699 - 152,131,164 (+)NCBI
Rnor_6.0X156,363,400 - 156,379,035 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602023   ⟹   XP_017457512
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X156,363,400 - 156,379,433 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099684   ⟹   XP_038955612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X152,115,699 - 152,131,164 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101051   ⟸   NM_001107581
- Peptide Label: precursor
- UniProtKB: D3ZPX4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006229639   ⟸   XM_006229577
- Peptide Label: isoform X1
- UniProtKB: D3ZPX4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771821   ⟸   XM_008773599
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008771820   ⟸   XM_008773598
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457512   ⟸   XM_017602023
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000068735   ⟸   ENSRNOT00000083148
RefSeq Acc Id: XP_038955612   ⟸   XM_039099684
- Peptide Label: isoform X3
Protein Domains
IPT/TIG   Sema

Transcriptome

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

Promoters
RGD ID:13702042
Promoter ID:EPDNEW_R12566
Type:single initiation site
Name:Plxna3_1
Description:plexin A3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X156,379,189 - 156,379,249EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 156372143 156372144 A C snv SR/JrHsd (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 160274207 160274208 G C snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584973 AgrOrtholog
Ensembl Genes ENSRNOG00000060464 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000068735 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000083148 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
  2.60.40.10 UniProtKB/Swiss-Prot
InterPro Ig-like_fold UniProtKB/Swiss-Prot
  Ig_E-set UniProtKB/Swiss-Prot
  IPT_dom UniProtKB/Swiss-Prot
  Plexin UniProtKB/Swiss-Prot
  Plexin_cytoplasmic_RasGAP_dom UniProtKB/Swiss-Prot
  Plexin_repeat UniProtKB/Swiss-Prot
  PSI UniProtKB/Swiss-Prot
  Rho_GTPase_activation_prot UniProtKB/Swiss-Prot
  Semap_dom UniProtKB/Swiss-Prot
  Semap_dom_sf UniProtKB/Swiss-Prot
  TIG1_plexin UniProtKB/Swiss-Prot
  TIG2_plexin UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:309280 UniProtKB/Swiss-Prot
NCBI Gene 309280 ENTREZGENE
PANTHER PTHR22625 UniProtKB/Swiss-Prot
Pfam Plexin_cytopl UniProtKB/Swiss-Prot
  PSI UniProtKB/Swiss-Prot
  Sema UniProtKB/Swiss-Prot
  TIG UniProtKB/Swiss-Prot
  TIG_2 UniProtKB/Swiss-Prot
  TIG_plexin UniProtKB/Swiss-Prot
PhenoGen Plxna3 PhenoGen
PROSITE SEMA UniProtKB/Swiss-Prot
SMART IPT UniProtKB/Swiss-Prot
  PSI UniProtKB/Swiss-Prot
  Sema UniProtKB/Swiss-Prot
Superfamily-SCOP SSF101912 UniProtKB/Swiss-Prot
  SSF48350 UniProtKB/Swiss-Prot
  SSF81296 UniProtKB/Swiss-Prot
UniProt D3ZPX4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-13   plexin A3  Plxna3  plexin A3 (mapped)  Name updated 737654 APPROVED
2007-04-11 Plxna3  plexin A3 (mapped)  Plxna3_mapped  plexin A3 (mapped)  Data Merged 737654 APPROVED
2006-11-19 Plxna3  plexin A3 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Plxna3_mapped  plexin A3 (mapped)  Plxna3  plexin A3  Symbol and Name updated 1556543 APPROVED
2003-04-09 Plxna3  plexin A3  Plxn4  Plexin 4  Symbol and Name updated 629477 APPROVED
2002-06-10 Plxn4  Plexin 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology mouse homolog Plexin-A3 receptor is activated by and mediates semaphorin signalling to trigger stereotyped pruning of specific hippocampal mossy fiber and pyramidal axon branches 1303935
gene_homology mouse homolog Plexin-A3 receptor is activated by and mediates semaphorin signalling to trigger stereotyped pruning of specific hippocampal mossy fiber and pyramidal axon branches 1303936