Epm2a (EPM2A glucan phosphatase, laforin) - Rat Genome Database

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Gene: Epm2a (EPM2A glucan phosphatase, laforin) Rattus norvegicus
Analyze
Symbol: Epm2a
Name: EPM2A glucan phosphatase, laforin
RGD ID: 71047
Description: Predicted to have several functions, including glycogen (starch) synthase activity; phosphatase activity; and polysaccharide binding activity. Predicted to be involved in several processes, including dephosphorylation; regulation of cellular protein localization; and regulation of cellular protein metabolic process. Predicted to colocalize with polysome. Human ortholog(s) of this gene implicated in Lafora disease and progressive myoclonus epilepsy. Orthologous to human EPM2A (EPM2A glucan phosphatase, laforin); INTERACTS WITH 1,2-dimethylhydrazine; aconitine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: epilepsy, progressive myoclonic epilepsy, type 2 gene alpha; epilepsy, progressive myoclonus type 2A; EPM2A, laforin glucan phosphatase; glucan phosphatase; lafora PTPase; laforin; LAFPTPase; LOC684363; similar to Laforin (Lafora PTPase) (LAFPTPase)
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
mRatBN7.215,727,111 - 5,845,338 (+)NCBI
Rnor_6.0 Ensembl15,448,958 - 5,571,512 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015,448,958 - 5,571,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.017,100,639 - 7,223,403 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.116,051,557 - 6,172,313 (+)NCBI
Celera14,243,803 - 4,360,561 (+)NCBICelera
Cytogenetic Map1p13NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
autophagosome assembly  (ISO)
autophagy  (ISO)
calcium ion transport  (ISO)
carbohydrate phosphorylation  (ISO)
cellular macromolecule metabolic process  (ISO)
dephosphorylation  (ISO,ISS)
glial cell proliferation  (ISO)
glycogen biosynthetic process  (ISO)
glycogen metabolic process  (ISO,ISS)
habituation  (ISO)
L-glutamate transmembrane transport  (ISO)
mitochondrion organization  (ISO)
negative regulation of cell cycle  (ISO)
negative regulation of dephosphorylation  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of peptidyl-serine phosphorylation  (ISO)
negative regulation of phosphatase activity  (ISO)
negative regulation of TOR signaling  (ISO)
nervous system development  (ISO)
peptidyl-tyrosine dephosphorylation  (IEA,ISO)
phosphorylated carbohydrate dephosphorylation  (ISO,ISS)
positive regulation of macroautophagy  (ISO)
proteasome-mediated ubiquitin-dependent protein catabolic process  (ISO)
protein dephosphorylation  (ISO)
regulation of cell growth  (ISO)
regulation of gene expression  (ISO)
regulation of glycogen (starch) synthase activity  (ISO)
regulation of phosphorylation  (ISO)
regulation of proteasomal protein catabolic process  (ISO)
regulation of protein import into nucleus  (ISO)
regulation of protein kinase activity  (ISO)
regulation of protein localization to plasma membrane  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of protein ubiquitination  (ISO)
regulation of ubiquitin protein ligase activity  (ISO)
Wnt signaling pathway  (ISO)

Cellular Component

References

Additional References at PubMed
PMID:11001928   PMID:11739371   PMID:12019206   PMID:12915448   PMID:15102711   PMID:15541350   PMID:16901901   PMID:16971387   PMID:17908927   PMID:18040046   PMID:18617530   PMID:18824542  
PMID:18852261   PMID:20453062   PMID:21552327   PMID:23663739   PMID:24430976   PMID:24914213   PMID:25416783   PMID:25538239   PMID:25544560   PMID:26316108   PMID:26976331   PMID:27107699  
PMID:28063983   PMID:28536304   PMID:28973665  


Genomics

Comparative Map Data
Epm2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.215,727,111 - 5,845,338 (+)NCBI
Rnor_6.0 Ensembl15,448,958 - 5,571,512 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015,448,958 - 5,571,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.017,100,639 - 7,223,403 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.116,051,557 - 6,172,313 (+)NCBI
Celera14,243,803 - 4,360,561 (+)NCBICelera
Cytogenetic Map1p13NCBI
EPM2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6145,382,535 - 145,736,023 (-)EnsemblGRCh38hg38GRCh38
GRCh386145,382,540 - 145,736,023 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376145,946,441 - 146,057,159 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366145,988,133 - 146,098,684 (-)NCBINCBI36hg18NCBI36
Build 346145,988,132 - 146,098,684NCBI
Celera6146,686,800 - 146,797,348 (-)NCBI
Cytogenetic Map6q24.3NCBI
HuRef6143,510,000 - 143,620,189 (-)NCBIHuRef
CHM1_16146,209,644 - 146,320,201 (-)NCBICHM1_1
Epm2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391011,218,435 - 11,335,408 (+)NCBIGRCm39mm39
GRCm39 Ensembl1011,219,148 - 11,335,388 (+)Ensembl
GRCm381011,342,691 - 11,459,664 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1011,343,404 - 11,459,644 (+)EnsemblGRCm38mm10GRCm38
MGSCv371011,063,243 - 11,177,275 (+)NCBIGRCm37mm9NCBIm37
MGSCv361011,033,594 - 11,147,912 (+)NCBImm8
Celera1011,232,470 - 11,346,997 (+)NCBICelera
Cytogenetic Map10A1NCBI
Epm2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543614,926,123 - 14,983,180 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543614,925,452 - 14,982,357 (+)NCBIChiLan1.0ChiLan1.0
EPM2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16148,133,563 - 148,238,519 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v06143,179,097 - 143,525,223 (-)NCBIMhudiblu_PPA_v0panPan3
EPM2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1136,835,775 - 36,977,653 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl136,870,594 - 36,931,847 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha137,577,467 - 37,858,360 (-)NCBI
ROS_Cfam_1.0136,862,309 - 37,141,316 (-)NCBI
UMICH_Zoey_3.1136,732,602 - 37,013,661 (-)NCBI
UNSW_CanFamBas_1.0136,604,089 - 36,884,723 (-)NCBI
UU_Cfam_GSD_1.0137,104,772 - 37,201,859 (-)NCBI
Epm2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946131,813,991 - 131,874,561 (-)NCBI
SpeTri2.0NW_004936625761,013 - 819,826 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EPM2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl119,755,720 - 20,024,398 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1119,806,363 - 19,893,350 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2122,050,546 - 22,135,943 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EPM2A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11326,152,974 - 26,266,676 (+)NCBI
ChlSab1.1 Ensembl1326,153,319 - 26,264,568 (+)Ensembl
Epm2a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247538,715,898 - 8,805,728 (+)NCBI

Position Markers
Z19543  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215,763,936 - 5,764,130 (+)MAPPER
Rnor_6.015,486,427 - 5,486,620NCBIRnor6.0
Rnor_5.017,138,084 - 7,138,277UniSTSRnor5.0
RGSC_v3.416,089,883 - 6,090,076UniSTSRGSC3.4
Celera14,280,330 - 4,280,523UniSTS
Cytogenetic Map1p1UniSTS
G47430  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.215,827,147 - 5,827,359 (+)MAPPER
Rnor_6.015,553,527 - 5,553,738NCBIRnor6.0
Rnor_5.017,205,609 - 7,205,820UniSTSRnor5.0
RGSC_v3.416,153,515 - 6,153,726UniSTSRGSC3.4
Celera14,343,091 - 4,343,302UniSTS
Cytogenetic Map1p1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124368159Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128468970Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1383915911314658Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:269
Count of miRNA genes:170
Interacting mature miRNAs:214
Transcripts:ENSRNOT00000061930
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 4 5 5 4
Low 1 43 36 23 16 23 4 6 69 35 41 11 4
Below cutoff 2 21 18 3 18

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061930   ⟹   ENSRNOP00000058646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15,448,958 - 5,571,512 (+)Ensembl
RefSeq Acc Id: NM_001276762   ⟹   NP_001263691
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.215,727,111 - 5,845,103 (+)NCBI
Rnor_6.015,448,958 - 5,571,512 (+)NCBI
Rnor_5.017,100,639 - 7,223,403 (+)NCBI
Celera14,243,803 - 4,360,561 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106219   ⟹   XP_038962147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.215,785,761 - 5,845,338 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001263691 (Get FASTA)   NCBI Sequence Viewer  
  XP_038962147 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK60619 (Get FASTA)   NCBI Sequence Viewer  
  EDL93717 (Get FASTA)   NCBI Sequence Viewer  
  Q91XQ2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001263691   ⟸   NM_001276762
- UniProtKB: Q91XQ2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058646   ⟸   ENSRNOT00000061930
RefSeq Acc Id: XP_038962147   ⟸   XM_039106219
- Peptide Label: isoform X1
Protein Domains
CBM20   Tyrosine-protein phosphatase

Transcriptome

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

Promoters
RGD ID:13689490
Promoter ID:EPDNEW_R15
Type:single initiation site
Name:Epm2a_1
Description:EPM2A, laforin glucan phosphatase
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_6.015,448,932 - 5,448,992EPDNEW

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71047 AgrOrtholog
Ensembl Genes ENSRNOG00000040242 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000058646 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000061930 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.90.190.10 UniProtKB/Swiss-Prot
InterPro Carb-bd-like_fold UniProtKB/Swiss-Prot
  CBM20_laforin UniProtKB/Swiss-Prot
  CBM_fam20 UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Laforin UniProtKB/Swiss-Prot
  Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot
  Tyr_Pase_AS UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_DUAL_dom UniProtKB/Swiss-Prot
KEGG Report rno:114005 UniProtKB/Swiss-Prot
NCBI Gene 114005 ENTREZGENE
PANTHER PTHR46864 UniProtKB/Swiss-Prot
Pfam CBM_20 UniProtKB/Swiss-Prot
PhenoGen Epm2a PhenoGen
PROSITE CBM20 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_DUAL UniProtKB/Swiss-Prot
SMART CBM_2 UniProtKB/Swiss-Prot
  DSPc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49452 UniProtKB/Swiss-Prot
  SSF52799 UniProtKB/Swiss-Prot
UniProt EPM2A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F1LPW7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Epm2a  EPM2A glucan phosphatase, laforin  Epm2a  EPM2A, laforin glucan phosphatase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-08-18 Epm2a  EPM2A, laforin glucan phosphatase  Epm2a  epilepsy, progressive myoclonus type 2A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-17 Epm2a  epilepsy, progressive myoclonus type 2A  LOC684363  similar to Laforin (Lafora PTPase) (LAFPTPase)  Data Merged 737654 PROVISIONAL
2009-12-15 Epm2a  epilepsy, progressive myoclonus type 2A  Epm2a  epilepsy, progressive myoclonic epilepsy, type 2 gene alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC684363  similar to Laforin (Lafora PTPase) (LAFPTPase)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-07-09 Epm2a  epilepsy, progressive myoclonic epilepsy, type 2 gene alpha      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations are associated with Lafora's disease, an autosomal recessive progressive myoclonus epilepsy 70733
gene_expression present in the cerebellum, hippocampus, cerebral cortex, and the olfactory bulb, expression is highest in the adults 70733
gene_homology 94% similar to the human and mouse ortholog 70733
gene_process involved in maturation and growth of the neural tissues 70733