Plxna2 (plexin A2) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Plxna2 (plexin A2) Rattus norvegicus
Analyze
Symbol: Plxna2
Name: plexin A2
RGD ID: 1305325
Description: Predicted to have identical protein binding activity and semaphorin receptor activity. Predicted to be involved in several processes, including chordate embryonic development; limb bud formation; and nervous system development. Predicted to localize to integral component of plasma membrane and semaphorin receptor complex. Orthologous to human PLXNA2 (plexin A2); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC289392; plexin-A2
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
Rnor_6.013113,373,569 - 113,570,774 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13113,373,578 - 113,571,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013117,922,569 - 118,118,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413110,555,958 - 110,754,672 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113110,745,080 - 110,943,775 (+)NCBI
Celera13105,589,023 - 105,784,376 (+)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-Chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
buta-1,3-diene  (ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ferroheme b  (ISO)
folic acid  (ISO)
furan  (EXP)
geldanamycin  (ISO)
genistein  (ISO)
glafenine  (EXP)
heme b  (ISO)
ketamine  (EXP)
methapyrilene  (ISO)
methotrexate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
nickel sulfate  (ISO)
nimesulide  (EXP)
oxaliplatin  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)

References

Additional References at PubMed
PMID:18327254   PMID:19666519   PMID:20877282   PMID:20881961  


Genomics

Comparative Map Data
Plxna2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.013113,373,569 - 113,570,774 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13113,373,578 - 113,571,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013117,922,569 - 118,118,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413110,555,958 - 110,754,672 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113110,745,080 - 110,943,775 (+)NCBI
Celera13105,589,023 - 105,784,376 (+)NCBICelera
Cytogenetic Map13q27NCBI
PLXNA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1208,022,242 - 208,244,384 (-)EnsemblGRCh38hg38GRCh38
GRCh381208,022,242 - 208,244,384 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371208,195,587 - 208,417,665 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361206,262,210 - 206,484,288 (-)NCBINCBI36hg18NCBI36
Build 341204,588,613 - 204,805,511NCBI
Celera1181,426,043 - 181,648,153 (-)NCBI
Cytogenetic Map1q32.2NCBI
HuRef1178,869,811 - 179,092,243 (-)NCBIHuRef
CHM1_11209,467,937 - 209,690,032 (-)NCBICHM1_1
Plxna2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,302,020 - 194,499,177 (+)NCBIGRCm39mm39
GRCm381194,619,791 - 194,816,869 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,618,218 - 194,816,869 (+)EnsemblGRCm38mm10GRCm38
MGSCv371196,446,023 - 196,643,063 (+)NCBIGRCm37mm9NCBIm37
MGSCv361196,320,645 - 196,513,298 (+)NCBImm8
Celera1201,520,017 - 201,716,761 (+)NCBICelera
Cytogenetic Map1H6NCBI
Plxna2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554893,914,633 - 4,116,825 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554893,914,137 - 4,116,780 (+)NCBIChiLan1.0ChiLan1.0
PLXNA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11188,408,041 - 188,654,934 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1188,408,048 - 188,603,208 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01183,600,533 - 183,848,418 (-)NCBIMhudiblu_PPA_v0panPan3
PLXNA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl76,863,663 - 7,049,250 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.176,863,518 - 7,049,301 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Plxna2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365574,808,371 - 4,920,453 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLXNA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9134,584,406 - 134,796,064 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19134,584,760 - 134,800,471 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29148,294,163 - 148,333,326 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLXNA2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2521,202,014 - 21,419,521 (+)Ensembl
ChlSab1.12521,201,867 - 21,424,529 (+)NCBI
Plxna2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248073,643,283 - 3,829,817 (+)NCBI

Position Markers
D13Got103  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013113,442,390 - 113,442,606NCBIRnor6.0
Rnor_5.013117,991,248 - 117,991,464UniSTSRnor5.0
RGSC_v3.413110,631,019 - 110,631,236RGDRGSC3.4
RGSC_v3.413110,631,020 - 110,631,236UniSTSRGSC3.4
RGSC_v3.113110,820,124 - 110,820,340RGD
Celera13105,657,646 - 105,657,862UniSTS
Cytogenetic Map13q27UniSTS
RH 3.4 Map13757.6RGD
RH 3.4 Map13757.6UniSTS
RH 2.0 Map13767.8RGD
D13Got114  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013113,390,042 - 113,390,330NCBIRnor6.0
Rnor_5.013117,939,098 - 117,939,386UniSTSRnor5.0
RGSC_v3.413110,574,962 - 110,575,251RGDRGSC3.4
RGSC_v3.413110,574,963 - 110,575,251UniSTSRGSC3.4
RGSC_v3.113110,764,067 - 110,764,355RGD
Celera13105,605,490 - 105,605,778UniSTS
Cytogenetic Map13q27UniSTS
RH 3.4 Map13759.6RGD
RH 3.4 Map13759.6UniSTS
RH 2.0 Map13775.6RGD
AW457381  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013113,566,968 - 113,567,055NCBIRnor6.0
Rnor_5.013118,114,587 - 118,114,674UniSTSRnor5.0
RGSC_v3.413110,752,431 - 110,752,518UniSTSRGSC3.4
Celera13105,780,570 - 105,780,657UniSTS
Cytogenetic Map13q27UniSTS
BE114222  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013113,478,232 - 113,478,387NCBIRnor6.0
Rnor_5.013118,025,851 - 118,026,006UniSTSRnor5.0
RGSC_v3.413110,663,695 - 110,663,850UniSTSRGSC3.4
Celera13105,691,809 - 105,691,964UniSTS
Cytogenetic Map13q27UniSTS
RH 3.4 Map13794.8UniSTS
MARC_9713-9714:996688545:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013113,555,021 - 113,555,780NCBIRnor6.0
Rnor_5.013118,102,640 - 118,103,399UniSTSRnor5.0
RGSC_v3.413110,740,484 - 110,741,243UniSTSRGSC3.4
Celera13105,768,621 - 105,769,380UniSTS
Cytogenetic Map13q27UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:562
Count of miRNA genes:243
Interacting mature miRNAs:358
Transcripts:ENSRNOT00000009900
Prediction methods:Miranda, 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 23 23 23 1 1 74 28 20 11 1
Low 3 43 34 18 19 18 7 10 7 16 7
Below cutoff 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009900   ⟹   ENSRNOP00000009900
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13113,373,578 - 113,571,648 (+)Ensembl
RefSeq Acc Id: NM_001105988   ⟹   NP_001099458
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013113,373,569 - 113,570,774 (+)NCBI
Rnor_5.013117,922,569 - 118,118,393 (+)NCBI
RGSC_v3.413110,555,958 - 110,754,672 (+)RGD
Celera13105,589,023 - 105,784,376 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099458 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95045 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099458   ⟸   NM_001105988
- UniProtKB: D3ZWP6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009900   ⟸   ENSRNOT00000009900
Protein Domains
Sema

Transcriptome

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

Promoters
RGD ID:13699130
Promoter ID:EPDNEW_R9655
Type:multiple initiation site
Name:Plxna2_1
Description:plexin A2
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_6.013113,373,565 - 113,373,625EPDNEW

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)
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/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/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
WKY/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
WKY/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
WKY/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
WN/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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 113402917 113402918 A C snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305325 AgrOrtholog
Ensembl Genes ENSRNOG00000007324 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009900 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009900 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_fold UniProtKB/TrEMBL
  Ig_E-set UniProtKB/TrEMBL
  IPT_TIG_rcpt UniProtKB/TrEMBL
  Plexin UniProtKB/TrEMBL
  Plexin-A2_sema UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  Plexin_cytoplasmic_RasGAP_dom UniProtKB/TrEMBL
  Plexin_repeat UniProtKB/TrEMBL
  Rho_GTPase_activation_prot UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
  TIG1_plexin UniProtKB/TrEMBL
  TIG2_plexin UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
KEGG Report rno:289392 UniProtKB/TrEMBL
NCBI Gene 289392 ENTREZGENE
PANTHER PTHR22625 UniProtKB/TrEMBL
Pfam Plexin_cytopl UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  TIG UniProtKB/TrEMBL
  TIG_2 UniProtKB/TrEMBL
  TIG_plexin UniProtKB/TrEMBL
PhenoGen Plxna2 PhenoGen
PROSITE SEMA UniProtKB/TrEMBL
SMART IPT UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
Superfamily-SCOP Ig_E-set UniProtKB/TrEMBL
  Rho_GAP UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
UniGene Rn.205178 ENTREZGENE
UniProt D3ZWP6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Plxna2  plexin A2   Plxna2_predicted  plexin A2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Plxna2_predicted  plexin A2 (predicted)      Symbol and Name status set to approved 70820 APPROVED