Slmap (sarcolemma associated protein) - Rat Genome Database

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Gene: Slmap (sarcolemma associated protein) Rattus norvegicus
Analyze
Symbol: Slmap
Name: sarcolemma associated protein
RGD ID: 1307674
Description: Predicted to be involved in protein localization to plasma membrane; regulation of membrane depolarization during cardiac muscle cell action potential; and regulation of voltage-gated sodium channel activity. Predicted to be integral component of membrane. Orthologous to human SLMAP (sarcolemma associated protein); INTERACTS WITH acrylamide; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC290533; sarcolemmal membrane-associated protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2161,667,205 - 1,785,200 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl161,667,208 - 1,785,149 (-)Ensembl
Rnor_6.0162,112,271 - 2,227,336 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,112,274 - 2,227,309 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,087,744 - 2,201,812 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,707,264 - 1,822,281 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1161,708,665 - 1,846,767 (-)NCBI
Celera161,641,356 - 1,755,574 (-)NCBICelera
Cytogenetic Map16p16NCBI
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

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10986292   PMID:12477932   PMID:15057822   PMID:23064965   PMID:25743393   PMID:30856349  


Genomics

Comparative Map Data
Slmap
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2161,667,205 - 1,785,200 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl161,667,208 - 1,785,149 (-)Ensembl
Rnor_6.0162,112,271 - 2,227,336 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,112,274 - 2,227,309 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,087,744 - 2,201,812 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,707,264 - 1,822,281 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1161,708,665 - 1,846,767 (-)NCBI
Celera161,641,356 - 1,755,574 (-)NCBICelera
Cytogenetic Map16p16NCBI
SLMAP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl357,755,450 - 57,930,003 (+)EnsemblGRCh38hg38GRCh38
GRCh38357,756,229 - 57,930,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37357,742,036 - 57,915,740 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36357,718,214 - 57,889,934 (+)NCBINCBI36hg18NCBI36
Build 34357,718,213 - 57,889,934NCBI
Celera357,757,094 - 57,928,809 (+)NCBI
Cytogenetic Map3p14.3NCBI
HuRef357,840,319 - 58,012,336 (+)NCBIHuRef
CHM1_1357,693,425 - 57,865,092 (+)NCBICHM1_1
Slmap
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391426,134,323 - 26,256,103 (-)NCBIGRCm39mm39
GRCm39 Ensembl1426,134,323 - 26,256,086 (-)Ensembl
GRCm381426,413,168 - 26,534,624 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,413,168 - 26,534,931 (-)EnsemblGRCm38mm10GRCm38
MGSCv371427,232,661 - 27,353,226 (-)NCBIGRCm37mm9NCBIm37
MGSCv361425,246,359 - 25,366,924 (-)NCBImm8
Celera1422,656,214 - 22,777,124 (-)NCBICelera
Cytogenetic Map14A3NCBI
Slmap
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554307,471,400 - 7,622,459 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554307,470,823 - 7,620,101 (+)NCBIChiLan1.0ChiLan1.0
SLMAP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1359,108,247 - 59,280,713 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl359,108,247 - 59,280,713 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0357,688,669 - 57,864,355 (+)NCBIMhudiblu_PPA_v0panPan3
SLMAP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12032,592,576 - 32,738,515 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2032,594,417 - 32,738,823 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2032,521,391 - 32,667,566 (-)NCBI
ROS_Cfam_1.02032,865,997 - 33,012,696 (-)NCBI
UMICH_Zoey_3.12032,321,432 - 32,468,023 (-)NCBI
UNSW_CanFamBas_1.02032,678,316 - 32,826,357 (-)NCBI
UU_Cfam_GSD_1.02032,850,352 - 32,996,713 (-)NCBI
LOC101964904
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118174,918,976 - 175,069,993 (+)NCBI
SpeTri2.0NW_0049364738,057,236 - 8,208,564 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLMAP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1339,571,987 - 39,721,895 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11339,571,930 - 39,720,229 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21343,454,259 - 43,545,298 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103227801
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12219,054,322 - 19,231,037 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2219,054,673 - 19,232,336 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041147,635,320 - 147,814,440 (-)NCBIVero_WHO_p1.0
Slmap
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624821493,902 - 638,553 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D16Chm74  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,737,795 - 1,738,012 (+)MAPPERmRatBN7.2
Rnor_6.0162,182,833 - 2,183,049NCBIRnor6.0
Rnor_5.0162,157,324 - 2,157,540UniSTSRnor5.0
RGSC_v3.4161,776,438 - 1,776,654UniSTSRGSC3.4
Celera161,710,543 - 1,710,759UniSTS
Cytogenetic Map16p16UniSTS
RH98947  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,668,517 - 1,668,669 (+)MAPPERmRatBN7.2
Rnor_6.0162,113,584 - 2,113,735NCBIRnor6.0
Rnor_5.0162,089,057 - 2,089,208UniSTSRnor5.0
RGSC_v3.4161,706,870 - 1,707,021UniSTSRGSC3.4
Celera161,640,962 - 1,641,113UniSTS
Cytogenetic Map16p16UniSTS
AA875412  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,668,060 - 1,668,270 (+)MAPPERmRatBN7.2
Rnor_6.0162,113,127 - 2,113,336NCBIRnor6.0
Rnor_5.0162,088,600 - 2,088,809UniSTSRnor5.0
RGSC_v3.4161,706,413 - 1,706,622UniSTSRGSC3.4
Celera161,640,505 - 1,640,714UniSTS
RH 3.4 Map1616.3UniSTS
Cytogenetic Map16p16UniSTS
MARC_17013-17014:1023291181:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,718,281 - 1,718,704 (+)MAPPERmRatBN7.2
Rnor_6.0162,163,319 - 2,163,741NCBIRnor6.0
Rnor_5.0162,137,810 - 2,138,232UniSTSRnor5.0
RGSC_v3.4161,756,924 - 1,757,346UniSTSRGSC3.4
Celera161,691,028 - 1,691,451UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)163802452995463Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)168323802995225Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)168323802995225Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)168323802995225Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)168323802995225Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)168323802995225Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)168323802995225Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:59
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000067464
Prediction methods: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 3 43 53 37 19 37 8 10 74 35 41 11 8
Low 4 4 4 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC168941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000067464   ⟹   ENSRNOP00000060405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,668,912 - 1,785,149 (-)Ensembl
Rnor_6.0 Ensembl162,113,978 - 2,227,309 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089377   ⟹   ENSRNOP00000071715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,667,208 - 1,785,098 (-)Ensembl
Rnor_6.0 Ensembl162,112,274 - 2,227,258 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091513   ⟹   ENSRNOP00000069804
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,668,912 - 1,785,149 (-)Ensembl
Rnor_6.0 Ensembl162,115,375 - 2,226,121 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094174   ⟹   ENSRNOP00000078785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,667,208 - 1,785,098 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097120   ⟹   ENSRNOP00000097616
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,667,208 - 1,785,098 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113231   ⟹   ENSRNOP00000092583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,667,208 - 1,785,098 (-)Ensembl
RefSeq Acc Id: NM_001106060   ⟹   NP_001099530
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,668,912 - 1,785,149 (-)NCBI
Rnor_6.0162,113,978 - 2,227,309 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
RGSC_v3.4161,707,264 - 1,822,281 (-)RGD
Celera161,641,356 - 1,755,574 (-)RGD
Sequence:
RefSeq Acc Id: XM_006252541   ⟹   XP_006252603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252542   ⟹   XP_006252604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,113,988 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252543   ⟹   XP_006252605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252544   ⟹   XP_006252606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252545   ⟹   XP_006252607
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252550   ⟹   XP_006252612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,336 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252553   ⟹   XP_006252615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,785,200 (-)NCBI
Rnor_6.0162,112,274 - 2,227,335 (-)NCBI
Rnor_5.0162,087,744 - 2,201,812 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770981   ⟹   XP_008769203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,205 - 1,723,322 (-)NCBI
Rnor_6.0162,112,274 - 2,168,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600014   ⟹   XP_017455503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,335 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600015   ⟹   XP_017455504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,335 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600016   ⟹   XP_017455505
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
Rnor_6.0162,112,274 - 2,227,335 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600019   ⟹   XP_017455508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,205 - 1,770,531 (-)NCBI
Rnor_6.0162,112,274 - 2,212,372 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094247   ⟹   XP_038950175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094248   ⟹   XP_038950176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094249   ⟹   XP_038950177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094250   ⟹   XP_038950178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094251   ⟹   XP_038950179
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094252   ⟹   XP_038950180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094253   ⟹   XP_038950181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094254   ⟹   XP_038950182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094255   ⟹   XP_038950183
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094256   ⟹   XP_038950184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094257   ⟹   XP_038950185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094258   ⟹   XP_038950186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094259   ⟹   XP_038950187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094260   ⟹   XP_038950188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094261   ⟹   XP_038950189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,207 - 1,784,003 (-)NCBI
RefSeq Acc Id: XM_039094262   ⟹   XP_038950190
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,667,205 - 1,770,531 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099530 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252603 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252604 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252605 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252606 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252607 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252612 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252615 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769203 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455503 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455504 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455505 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455508 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950175 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950176 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950177 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950178 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950179 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950180 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950181 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950182 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950183 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950184 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950185 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950186 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950187 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950188 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950189 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950190 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68941 (Get FASTA)   NCBI Sequence Viewer  
  EDL75077 (Get FASTA)   NCBI Sequence Viewer  
  P0C219 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099530   ⟸   NM_001106060
- UniProtKB: D3ZKE6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252615   ⟸   XM_006252553
- Peptide Label: isoform X24
- UniProtKB: B5DF63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252605   ⟸   XM_006252543
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006252606   ⟸   XM_006252544
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006252607   ⟸   XM_006252545
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006252612   ⟸   XM_006252550
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_006252603   ⟸   XM_006252541
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252604   ⟸   XM_006252542
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008769203   ⟸   XM_008770981
- Peptide Label: isoform X26
- Sequence:
RefSeq Acc Id: XP_017455503   ⟸   XM_017600014
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017455504   ⟸   XM_017600015
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017455505   ⟸   XM_017600016
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017455508   ⟸   XM_017600019
- Peptide Label: isoform X27
- Sequence:
RefSeq Acc Id: ENSRNOP00000060405   ⟸   ENSRNOT00000067464
RefSeq Acc Id: ENSRNOP00000071715   ⟸   ENSRNOT00000089377
RefSeq Acc Id: ENSRNOP00000069804   ⟸   ENSRNOT00000091513
RefSeq Acc Id: XP_038950190   ⟸   XM_039094262
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038950181   ⟸   XM_039094253
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038950189   ⟸   XM_039094261
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038950182   ⟸   XM_039094254
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038950186   ⟸   XM_039094258
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038950187   ⟸   XM_039094259
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038950178   ⟸   XM_039094250
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038950183   ⟸   XM_039094255
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038950175   ⟸   XM_039094247
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038950188   ⟸   XM_039094260
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038950179   ⟸   XM_039094251
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038950184   ⟸   XM_039094256
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038950176   ⟸   XM_039094248
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038950185   ⟸   XM_039094257
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038950177   ⟸   XM_039094249
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038950180   ⟸   XM_039094252
- Peptide Label: isoform X15
RefSeq Acc Id: ENSRNOP00000078785   ⟸   ENSRNOT00000094174
RefSeq Acc Id: ENSRNOP00000092583   ⟸   ENSRNOT00000113231
RefSeq Acc Id: ENSRNOP00000097616   ⟸   ENSRNOT00000097120
Protein Domains
FHA

Transcriptome

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

Promoters
RGD ID:13699898
Promoter ID:EPDNEW_R10417
Type:initiation region
Name:Slmap_1
Description:sarcolemma associated protein
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_6.0162,227,259 - 2,227,319EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (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)
ACI/EurMcwi (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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307674 AgrOrtholog
Ensembl Genes ENSRNOG00000011307 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060405 UniProtKB/TrEMBL
  ENSRNOP00000069804 UniProtKB/TrEMBL
  ENSRNOP00000071715 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067464 UniProtKB/TrEMBL
  ENSRNOT00000089377 UniProtKB/TrEMBL
  ENSRNOT00000091513 UniProtKB/TrEMBL
InterPro FHA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SLMAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:290533 UniProtKB/TrEMBL
NCBI Gene 290533 ENTREZGENE
PANTHER PTHR15715:SF22 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slmap PhenoGen
PROSITE FHA_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JWA5_RAT UniProtKB/TrEMBL
  B5DF63 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKE6 ENTREZGENE, UniProtKB/TrEMBL
  P0C219 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Slmap  sarcolemma associated protein   Slmap_predicted  sarcolemma associated protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slmap_predicted  sarcolemma associated protein (predicted)      Symbol and Name status set to approved 70820 APPROVED