Pls3 (plastin 3) - Rat Genome Database
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Gene: Pls3 (plastin 3) Rattus norvegicus
Analyze
Symbol: Pls3
Name: plastin 3
RGD ID: 621409
Description: Predicted to be a structural constituent of presynaptic actin cytoskeleton. Involved in inner ear auditory receptor cell differentiation. Localizes to stereocilium. Human ortholog(s) of this gene implicated in osteoporosis. Orthologous to human PLS3 (plastin 3); PARTICIPATES IN auditory mechanotransduction pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: plastin 3 (T-isoform); plastin-3; T-plastin
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
mRatBN7.2X111,589,193 - 111,683,908 (+)NCBI
Rnor_6.0 EnsemblX119,030,419 - 119,124,250 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X119,030,311 - 119,124,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X119,173,230 - 119,266,240 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X29,868,937 - 29,965,118 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X29,923,513 - 29,982,843 (-)NCBI
CeleraX110,881,127 - 110,971,056 (+)NCBICelera
Cytogenetic MapXq34NCBI
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-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
beauvericin  (ISO)
benzbromarone  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
bucladesine  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
cobalt dichloride  (ISO)
D-glucose  (ISO)
DDT  (EXP)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
enniatin  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
glafenine  (EXP)
glucose  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP,ISO)
L-ascorbic acid  (ISO)
L-ethionine  (EXP)
lithium atom  (EXP)
lithium hydride  (EXP)
manganese(II) chloride  (EXP)
medroxyprogesterone acetate  (ISO)
methapyrilene  (ISO)
methylmercury(1+)  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel sulfate  (ISO)
omeprazole  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
terbufos  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7655078   PMID:12477932   PMID:23263861   PMID:24088043  


Genomics

Comparative Map Data
Pls3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X111,589,193 - 111,683,908 (+)NCBI
Rnor_6.0 EnsemblX119,030,419 - 119,124,250 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X119,030,311 - 119,124,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X119,173,230 - 119,266,240 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X29,868,937 - 29,965,118 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X29,923,513 - 29,982,843 (-)NCBI
CeleraX110,881,127 - 110,971,056 (+)NCBICelera
Cytogenetic MapXq34NCBI
PLS3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX115,561,174 - 115,650,861 (+)EnsemblGRCh38hg38GRCh38
GRCh38X115,561,174 - 115,650,861 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X114,795,501 - 114,885,181 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X114,701,765 - 114,791,246 (+)NCBINCBI36hg18NCBI36
Build 34X114,618,488 - 114,707,970NCBI
CeleraX115,230,242 - 115,320,243 (+)NCBI
Cytogenetic MapXq23NCBI
HuRefX104,379,340 - 104,468,198 (+)NCBIHuRef
CHM1_1X114,706,001 - 114,796,082 (+)NCBICHM1_1
Pls3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X74,829,259 - 74,918,788 (-)NCBIGRCm39mm39
GRCm39 EnsemblX74,829,260 - 74,918,788 (-)Ensembl
GRCm38X75,785,653 - 75,875,182 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX75,785,654 - 75,875,182 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X73,030,993 - 73,120,509 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X72,038,383 - 72,127,258 (-)NCBImm8
CeleraX67,188,917 - 67,297,722 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
Pls3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955490122,328 - 221,388 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955490125,913 - 221,152 (-)NCBIChiLan1.0ChiLan1.0
PLS3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X115,160,032 - 115,250,144 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX115,160,032 - 115,250,144 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X104,656,110 - 104,745,702 (+)NCBIMhudiblu_PPA_v0panPan3
PLS3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX88,308,888 - 88,398,810 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X88,308,817 - 88,399,682 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pls3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936499246,042 - 335,440 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLS3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX94,885,118 - 94,971,664 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X94,885,098 - 94,971,664 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X109,452,808 - 109,539,961 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLS3
(Chlorocebus sabaeus - African green monkey)
No map positions available.
Pls3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624940120,073 - 216,522 (-)NCBI

Position Markers
RH139054  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X119,069,784 - 119,069,945NCBIRnor6.0
Rnor_5.0X119,211,762 - 119,211,923UniSTSRnor5.0
RGSC_v3.4X29,924,408 - 29,924,569UniSTSRGSC3.4
CeleraX110,920,170 - 110,920,331UniSTS
Cytogenetic MapXq14UniSTS
RH133212  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X119,061,936 - 119,062,144NCBIRnor6.0
Rnor_5.0X119,203,914 - 119,204,122UniSTSRnor5.0
RGSC_v3.4X29,932,209 - 29,932,417UniSTSRGSC3.4
CeleraX110,912,330 - 110,912,538UniSTS
Cytogenetic MapXq14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory 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)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory 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)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat
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:549
Count of miRNA genes:277
Interacting mature miRNAs:347
Transcripts:ENSRNOT00000060168
Prediction methods:Microtar, Miranda, Pita, Pita,Microtar, 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 3 43 38 23 18 23 7 8 74 35 34 11 7
Low 19 18 1 18 1 3 7 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060168   ⟹   ENSRNOP00000056912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX119,030,419 - 119,124,250 (+)Ensembl
RefSeq Acc Id: NM_031084   ⟹   NP_112346
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,589,301 - 111,683,897 (+)NCBI
Rnor_6.0X119,030,419 - 119,124,257 (+)NCBI
Rnor_5.0X119,173,230 - 119,266,240 (+)NCBI
RGSC_v3.4X29,868,937 - 29,965,118 (-)RGD
CeleraX110,881,127 - 110,971,056 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257434   ⟹   XP_006257496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,589,193 - 111,683,908 (+)NCBI
Rnor_6.0X119,030,311 - 119,124,268 (+)NCBI
Rnor_5.0X119,173,230 - 119,266,240 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257438   ⟹   XP_006257500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,623,522 - 111,683,908 (+)NCBI
Rnor_6.0X119,064,289 - 119,124,268 (+)NCBI
Rnor_5.0X119,173,230 - 119,266,240 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602163   ⟹   XP_017457652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,623,470 - 111,683,908 (+)NCBI
Rnor_6.0X119,064,288 - 119,124,268 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602164   ⟹   XP_017457653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,623,675 - 111,683,908 (+)NCBI
Rnor_6.0X119,065,041 - 119,124,268 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100089   ⟹   XP_038956017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,610,596 - 111,683,908 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_112346   ⟸   NM_031084
- UniProtKB: F1LPK7 (UniProtKB/TrEMBL),   Q562B2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257496   ⟸   XM_006257434
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257500   ⟸   XM_006257438
- Peptide Label: isoform X2
- UniProtKB: F1LPK7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457652   ⟸   XM_017602163
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457653   ⟸   XM_017602164
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000056912   ⟸   ENSRNOT00000060168
RefSeq Acc Id: XP_038956017   ⟸   XM_039100089
- Peptide Label: isoform X1
Protein Domains
Calponin-homology (CH)   EF-hand

Transcriptome

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

Promoters
RGD ID:13701972
Promoter ID:EPDNEW_R12496
Type:multiple initiation site
Name:Pls3_1
Description:plastin 3
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_6.0X119,030,430 - 119,030,490EPDNEW

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)
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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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/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
SHRSP/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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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/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 119109832 119109833 C T snv ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), WN/N (MCW), MR/N (MCW), WKY/N (MCW), M520/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621409 AgrOrtholog
Ensembl Genes ENSRNOG00000027520 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000056912 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060168 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7311086 IMAGE-MGC_LOAD
InterPro Actinin_actin-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CH-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CH_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fimbrin/Plastin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLS2/3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81748 UniProtKB/TrEMBL
MGC_CLONE MGC:109253 IMAGE-MGC_LOAD
NCBI Gene 81748 ENTREZGENE
PANTHER PTHR19961 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR19961:SF32 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00307 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pls3 PhenoGen
PROSITE ACTININ_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ACTININ_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50021 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00033 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47576 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LPK7 ENTREZGENE, UniProtKB/TrEMBL
  PLST_RAT UniProtKB/Swiss-Prot
  Q562B2 ENTREZGENE, UniProtKB/TrEMBL
  Q63598 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Pls3  plastin 3  Pls3  plastin 3 (T-isoform)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Pls3  plastin 3 (T-isoform)      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Pls3  plastin 3 (T-isoform)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in stereocilia in the developing cochlea 731234
gene_product member of the plastins/fimbrin family of actin bundling proteins 731234