Mtmr1 (myotubularin related protein 1) - Rat Genome Database
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Gene: Mtmr1 (myotubularin related protein 1) Rattus norvegicus
Analyze
Symbol: Mtmr1
Name: myotubularin related protein 1
RGD ID: 1306569
Description: Predicted to have phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity; phosphatidylinositol-3-phosphatase activity; and protein homodimerization activity. Predicted to be involved in phosphatidylinositol dephosphorylation and regulation of phosphatidylinositol dephosphorylation. Predicted to localize to cytoplasm and plasma membrane. Orthologous to human MTMR1 (myotubularin related protein 1); INTERACTS WITH benzo[a]pyrene; bisphenol A; decabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC317296; myotubularin-related protein 1
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
mRatBN7.218215,031 - 248,541 (+)NCBI
Rnor_6.0 Ensembl18291,780 - 325,377 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.018291,785 - 325,415 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018337,401 - 371,027 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418205,546 - 238,997 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.118205,641 - 237,603 (+)NCBI
Celera18210,086 - 243,538 (+)NCBICelera
Cytogenetic Map18p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO,ISS)
plasma membrane  (ISO,ISS)

References

Additional References at PubMed
PMID:11733541   PMID:12217958   PMID:12477932   PMID:16787938   PMID:27018598   PMID:30361391  


Genomics

Comparative Map Data
Mtmr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.218215,031 - 248,541 (+)NCBI
Rnor_6.0 Ensembl18291,780 - 325,377 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.018291,785 - 325,415 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018337,401 - 371,027 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418205,546 - 238,997 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.118205,641 - 237,603 (+)NCBI
Celera18210,086 - 243,538 (+)NCBICelera
Cytogenetic Map18p13NCBI
MTMR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX150,692,971 - 150,765,108 (+)EnsemblGRCh38hg38GRCh38
GRCh38X150,692,962 - 150,765,108 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X149,861,435 - 149,933,581 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X149,612,527 - 149,684,233 (+)NCBINCBI36hg18NCBI36
Build 34X149,532,414 - 149,604,136NCBI
CeleraX150,109,440 - 150,181,123 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX138,746,677 - 138,793,029 (+)NCBIHuRef
CHM1_1X149,736,187 - 149,807,919 (+)NCBICHM1_1
Mtmr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X70,408,332 - 70,462,802 (+)NCBIGRCm39mm39
GRCm39 EnsemblX70,408,366 - 70,462,802 (+)Ensembl
GRCm38X71,364,760 - 71,419,196 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX71,364,760 - 71,419,196 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X68,617,935 - 68,672,371 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X67,625,316 - 67,679,752 (+)NCBImm8
CeleraX62,344,835 - 62,399,305 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
Mtmr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554986,462,626 - 6,528,380 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554986,462,706 - 6,528,297 (+)NCBIChiLan1.0ChiLan1.0
MTMR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X150,281,374 - 150,346,900 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX150,279,183 - 150,346,900 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X140,343,740 - 140,415,134 (+)NCBIMhudiblu_PPA_v0panPan3
MTMR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX118,937,470 - 118,999,920 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X118,936,865 - 118,999,630 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Mtmr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367141,693,919 - 1,772,974 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MTMR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX122,394,921 - 122,453,905 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X122,394,768 - 122,455,266 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X140,009,688 - 140,070,233 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MTMR1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X125,276,674 - 125,354,065 (+)NCBI
ChlSab1.1 EnsemblX125,281,758 - 125,354,377 (+)Ensembl
Mtmr1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249231,073,009 - 1,143,183 (+)NCBI

Position Markers
BE114560  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018293,066 - 293,215NCBIRnor6.0
Rnor_5.018338,682 - 338,831UniSTSRnor5.0
RGSC_v3.418237,567 - 237,716UniSTSRGSC3.4
Celera18242,108 - 242,257UniSTS
RH 3.4 Map1835.0UniSTS
Cytogenetic Map18p13UniSTS
RH134574  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018322,282 - 322,468NCBIRnor6.0
Rnor_5.018367,898 - 368,084UniSTSRnor5.0
RGSC_v3.418208,455 - 208,641UniSTSRGSC3.4
Celera18212,995 - 213,181UniSTS
RH 3.4 Map1835.0UniSTS
Cytogenetic Map18p13UniSTS
RH139616  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018291,832 - 292,041NCBIRnor6.0
Rnor_5.018337,448 - 337,657UniSTSRnor5.0
RH 3.4 Map1835.5UniSTS
Cytogenetic Map18p13UniSTS
AI230194  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018298,559 - 298,768NCBIRnor6.0
Rnor_5.018344,175 - 344,384UniSTSRnor5.0
RGSC_v3.418232,014 - 232,223UniSTSRGSC3.4
Celera18236,554 - 236,763UniSTS
RH 3.4 Map1835.0UniSTS
Cytogenetic Map18p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125999214Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125999214Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:100
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000003638
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


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 21 40 24 19 24 4 7 74 35 41 11 4
Low 22 17 17 17 4 4 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003638   ⟹   ENSRNOP00000003638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl18291,785 - 325,377 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078032   ⟹   ENSRNOP00000069284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl18291,780 - 325,374 (-)Ensembl
RefSeq Acc Id: NM_001191725   ⟹   NP_001178654
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,089 - 248,541 (+)NCBI
Rnor_6.018291,785 - 325,377 (-)NCBI
Rnor_5.018337,401 - 371,027 (-)NCBI
Celera18210,086 - 243,538 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006254380   ⟹   XP_006254442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,415 (-)NCBI
Rnor_5.018337,401 - 371,027 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254381   ⟹   XP_006254443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,414 (-)NCBI
Rnor_5.018337,401 - 371,027 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600977   ⟹   XP_017456466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,415 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600978   ⟹   XP_017456467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 324,206 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600979   ⟹   XP_017456468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,225 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600980   ⟹   XP_017456469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,225 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600981   ⟹   XP_017456470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.018291,785 - 325,225 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039096935   ⟹   XP_038952863
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,034 - 248,541 (+)NCBI
RefSeq Acc Id: XM_039096936   ⟹   XP_038952864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,034 - 248,541 (+)NCBI
RefSeq Acc Id: XM_039096937   ⟹   XP_038952865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,379 - 248,541 (+)NCBI
RefSeq Acc Id: XM_039096938   ⟹   XP_038952866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,379 - 248,541 (+)NCBI
RefSeq Acc Id: XM_039096939   ⟹   XP_038952867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,379 - 248,541 (+)NCBI
RefSeq Acc Id: XM_039096940   ⟹   XP_038952868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,032 - 240,636 (+)NCBI
RefSeq Acc Id: XM_039096941   ⟹   XP_038952869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218215,031 - 238,419 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178654   ⟸   NM_001191725
- UniProtKB: D3ZKK5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254442   ⟸   XM_006254380
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006254443   ⟸   XM_006254381
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017456466   ⟸   XM_017600977
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456468   ⟸   XM_017600979
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017456470   ⟸   XM_017600981
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017456469   ⟸   XM_017600980
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017456467   ⟸   XM_017600978
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000069284   ⟸   ENSRNOT00000078032
RefSeq Acc Id: ENSRNOP00000003638   ⟸   ENSRNOT00000003638
RefSeq Acc Id: XP_038952869   ⟸   XM_039096941
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038952868   ⟸   XM_039096940
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038952864   ⟸   XM_039096936
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952863   ⟸   XM_039096935
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952866   ⟸   XM_039096938
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952865   ⟸   XM_039096937
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038952867   ⟸   XM_039096939
- Peptide Label: isoform X5
Transcriptome

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

Promoters
RGD ID:13700622
Promoter ID:EPDNEW_R11146
Type:multiple initiation site
Name:Mtmr1_1
Description:myotubularin related protein 1
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_6.018325,416 - 325,476EPDNEW

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)
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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
18 295487 295488 C T snv ACI/N (MCW), M520/N (MCW), F344/NRrrc (MCW), Buf/N (MCW)
18 306204 306205 C T snv ACI/N (MCW), WKY/N (MCW), MR/N (MCW), M520/N (MCW), F344/NRrrc (MCW), Buf/N (MCW)
18 309735 309736 T C snv M520/N (MCW), F344/NRrrc (MCW), WKY/N (MCW), ACI/N (MCW), MR/N (MCW), Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306569 AgrOrtholog
Ensembl Genes ENSRNOG00000002697 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003638 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069284 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003638 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078032 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro GRAM UniProtKB/TrEMBL
  MTMR1/MTMR2 UniProtKB/TrEMBL
  MTMR1_PH-GRAM UniProtKB/TrEMBL
  Myotub-related UniProtKB/TrEMBL
  Myotubularin_fam UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/TrEMBL
  Tyr/Dual-sp_Pase UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/TrEMBL
KEGG Report rno:317296 UniProtKB/TrEMBL
NCBI Gene 317296 ENTREZGENE
PANTHER PTHR10807 UniProtKB/TrEMBL
  PTHR10807:SF40 UniProtKB/TrEMBL
Pfam GRAM UniProtKB/TrEMBL
  Myotub-related UniProtKB/TrEMBL
PhenoGen Mtmr1 PhenoGen
PROSITE PPASE_MYOTUBULARIN UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/TrEMBL
SMART GRAM UniProtKB/TrEMBL
  PTPc_motif UniProtKB/TrEMBL
Superfamily-SCOP SSF52799 UniProtKB/TrEMBL
UniProt A0A0G2JUZ0_RAT UniProtKB/TrEMBL
  D3ZKK5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Mtmr1  myotubularin related protein 1   Mtmr1_predicted  myotubularin related protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Mtmr1_predicted  myotubularin related protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED