Limch1 (LIM and calponin homology domains 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Limch1 (LIM and calponin homology domains 1) Rattus norvegicus
Analyze
Symbol: Limch1
Name: LIM and calponin homology domains 1
RGD ID: 1305269
Description: Predicted to enable myosin II head/neck binding activity. Predicted to be involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Predicted to be active in stress fiber. Orthologous to human LIMCH1 (LIM and calponin homology domains 1); INTERACTS WITH (+)-schisandrin B; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LIM and calponin homology domains-containing protein 1; LOC305332; RGD1305269; similar to hypothetical 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
mRatBN7.21441,112,579 - 41,425,185 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
Rnor_6.01442,760,363 - 43,072,976 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,762,587 - 43,072,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,558,732 - 42,868,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,722,254 - 44,049,555 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11443,681,141 - 44,052,100 (-)NCBI
Celera1440,270,045 - 40,579,190 (-)NCBICelera
Cytogenetic Map14p11NCBI
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
(+)-schisandrin B  (EXP)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chlordecone  (ISO)
chloroprene  (EXP)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
etoposide  (ISO)
glyphosate  (EXP)
hexadecanoic acid  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
zinc dichloride  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:17291445   PMID:20607275   PMID:23106098   PMID:24625528   PMID:28228547   PMID:30361391  


Genomics

Comparative Map Data
Limch1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21441,112,579 - 41,425,185 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
Rnor_6.01442,760,363 - 43,072,976 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,762,587 - 43,072,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,558,732 - 42,868,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,722,254 - 44,049,555 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11443,681,141 - 44,052,100 (-)NCBI
Celera1440,270,045 - 40,579,190 (-)NCBICelera
Cytogenetic Map14p11NCBI
LIMCH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl441,359,607 - 41,700,044 (+)EnsemblGRCh38hg38GRCh38
GRCh38441,359,607 - 41,700,044 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37441,361,624 - 41,702,061 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36441,057,561 - 41,395,767 (+)NCBINCBI36hg18NCBI36
Celera441,806,095 - 42,146,075 (+)NCBI
Cytogenetic Map4p13NCBI
HuRef440,684,478 - 41,024,427 (+)NCBIHuRef
CHM1_1441,363,356 - 41,702,595 (+)NCBICHM1_1
Limch1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39566,902,078 - 67,214,502 (+)NCBIGRCm39mm39
GRCm39 Ensembl566,903,170 - 67,214,501 (+)Ensembl
GRCm38566,745,889 - 67,057,159 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl566,745,827 - 67,057,158 (+)EnsemblGRCm38mm10GRCm38
MGSCv37567,137,079 - 67,448,398 (+)NCBIGRCm37mm9NCBIm37
MGSCv36567,025,084 - 67,335,232 (+)NCBImm8
Celera564,048,465 - 64,361,964 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
Limch1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,983,842 - 6,305,014 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,984,027 - 6,305,014 (-)NCBIChiLan1.0ChiLan1.0
LIMCH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1441,533,508 - 41,873,694 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl441,533,560 - 41,873,694 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0435,685,904 - 36,025,582 (+)NCBIMhudiblu_PPA_v0panPan3
LIMCH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11338,518,653 - 38,816,804 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1338,518,644 - 38,814,369 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1338,495,198 - 38,793,400 (+)NCBI
ROS_Cfam_1.01339,008,734 - 39,307,552 (+)NCBI
UMICH_Zoey_3.11338,699,406 - 38,997,408 (+)NCBI
UNSW_CanFamBas_1.01338,809,648 - 39,105,367 (+)NCBI
UU_Cfam_GSD_1.01339,284,402 - 39,582,653 (+)NCBI
Limch1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528537,365,504 - 37,677,692 (-)NCBI
SpeTri2.0NW_0049364828,620,543 - 8,932,731 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIMCH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl832,433,030 - 32,792,546 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1832,433,035 - 32,792,553 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2834,048,380 - 34,408,111 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIMCH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,656,502 - 8,994,669 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl278,653,600 - 8,994,634 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604754,972,000 - 55,314,409 (-)NCBIVero_WHO_p1.0
Limch1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476125,375,501 - 25,706,756 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Rat15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,275,590 - 41,275,734 (+)MAPPERmRatBN7.2
Rnor_6.01442,924,142 - 42,924,285NCBIRnor6.0
Rnor_5.01442,722,129 - 42,722,272UniSTSRnor5.0
RGSC_v3.41443,898,015 - 43,898,159RGDRGSC3.4
RGSC_v3.41443,898,016 - 43,898,159UniSTSRGSC3.4
RGSC_v3.11443,900,406 - 43,900,550RGD
Celera1440,431,554 - 40,431,697UniSTS
RH 2.0 Map14451.1RGD
SHRSP x BN Map1428.3RGD
Cytogenetic Map14p11UniSTS
D14Got51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,366,647 - 41,366,913 (+)MAPPERmRatBN7.2
Rnor_6.01443,014,455 - 43,014,718NCBIRnor6.0
Rnor_5.01442,811,195 - 42,811,458UniSTSRnor5.0
RGSC_v3.41443,991,314 - 43,991,578RGDRGSC3.4
RGSC_v3.41443,991,315 - 43,991,578UniSTSRGSC3.4
RGSC_v3.11443,993,705 - 43,993,969RGD
Celera1440,522,492 - 40,522,755UniSTS
RH 2.0 Map14447.9RGD
Cytogenetic Map14p11UniSTS
SHGC-68207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,114,959 - 41,115,051 (+)MAPPERmRatBN7.2
Rnor_6.01442,762,744 - 42,762,835NCBIRnor6.0
Rnor_5.01442,561,113 - 42,561,204UniSTSRnor5.0
RGSC_v3.41443,724,637 - 43,724,728UniSTSRGSC3.4
Celera1440,270,202 - 40,270,293UniSTS
Cytogenetic Map14p11UniSTS
RH45623  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,376,531 - 41,376,709 (+)MAPPERmRatBN7.2
Rnor_6.01443,024,337 - 43,024,514NCBIRnor6.0
Rnor_5.01442,821,077 - 42,821,254UniSTSRnor5.0
RGSC_v3.41444,001,195 - 44,001,372UniSTSRGSC3.4
Celera1440,532,390 - 40,532,567UniSTS
Cytogenetic Map14p11UniSTS
RH133758  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,158,440 - 41,158,621 (+)MAPPERmRatBN7.2
Rnor_6.01442,805,924 - 42,806,104NCBIRnor6.0
Rnor_5.01442,604,687 - 42,604,867UniSTSRnor5.0
RGSC_v3.41443,768,803 - 43,768,983UniSTSRGSC3.4
Celera1440,313,187 - 40,313,367UniSTS
Cytogenetic Map14p11UniSTS
RH142364  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,114,655 - 41,114,810 (+)MAPPERmRatBN7.2
Rnor_6.01442,762,440 - 42,762,594NCBIRnor6.0
Rnor_5.01442,560,809 - 42,560,963UniSTSRnor5.0
RGSC_v3.41443,724,333 - 43,724,487UniSTSRGSC3.4
Celera1440,269,898 - 40,270,052UniSTS
Cytogenetic Map14p11UniSTS
BE102897  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,152,760 - 41,152,942 (+)MAPPERmRatBN7.2
Rnor_6.01442,800,244 - 42,800,425NCBIRnor6.0
Rnor_5.01442,599,007 - 42,599,188UniSTSRnor5.0
RGSC_v3.41443,763,123 - 43,763,304UniSTSRGSC3.4
Celera1440,307,563 - 40,307,744UniSTS
Cytogenetic Map14p11UniSTS
BI301572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,358,346 - 41,358,544 (+)MAPPERmRatBN7.2
Rnor_6.01443,005,828 - 43,006,025NCBIRnor6.0
Rnor_5.01442,804,091 - 42,804,288UniSTSRnor5.0
RGSC_v3.41443,983,239 - 43,983,436UniSTSRGSC3.4
Celera1440,514,158 - 40,514,355UniSTS
Cytogenetic Map14p11UniSTS
RH137678  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,423,717 - 41,423,933 (+)MAPPERmRatBN7.2
Rnor_6.01443,071,581 - 43,071,796NCBIRnor6.0
Rnor_5.01442,866,991 - 42,867,206UniSTSRnor5.0
RGSC_v3.41444,048,293 - 44,048,508UniSTSRGSC3.4
Celera1440,577,928 - 40,578,143UniSTS
Cytogenetic Map14p11UniSTS
RH138802  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,113,740 - 41,113,898 (+)MAPPERmRatBN7.2
Rnor_6.01442,761,525 - 42,761,682NCBIRnor6.0
Rnor_5.01442,559,894 - 42,560,051UniSTSRnor5.0
RGSC_v3.41443,723,418 - 43,723,575UniSTSRGSC3.4
Celera1440,268,983 - 40,269,140UniSTS
Cytogenetic Map14p11UniSTS
AI013730  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,115,246 - 41,115,426 (+)MAPPERmRatBN7.2
Rnor_6.01442,763,031 - 42,763,210NCBIRnor6.0
Rnor_5.01442,561,400 - 42,561,579UniSTSRnor5.0
RGSC_v3.41443,724,924 - 43,725,103UniSTSRGSC3.4
Celera1440,270,489 - 40,270,668UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:231
Count of miRNA genes:156
Interacting mature miRNAs:190
Transcripts:ENSRNOT00000064263
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 42 4 2 2 8 11 74 35 31 11 8
Low 3 1 51 37 19 37 10
Below cutoff 2 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ226534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000064263   ⟹   ENSRNOP00000063345
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
Rnor_6.0 Ensembl1442,762,587 - 43,072,843 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095221   ⟹   ENSRNOP00000076732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097408   ⟹   ENSRNOP00000097815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,198,052 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100682   ⟹   ENSRNOP00000096454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,120,773 - 41,282,803 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103342   ⟹   ENSRNOP00000093427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114959   ⟹   ENSRNOP00000093239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118493   ⟹   ENSRNOP00000087540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,114,803 - 41,425,191 (-)Ensembl
RefSeq Acc Id: NM_001191678   ⟹   NP_001178607
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,114,803 - 41,424,980 (-)NCBI
Rnor_6.01442,762,587 - 43,072,843 (-)NCBI
Rnor_5.01442,558,732 - 42,868,387 (-)NCBI
Celera1440,270,045 - 40,579,190 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599187   ⟹   XP_017454676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
Rnor_6.01442,760,363 - 43,072,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599188   ⟹   XP_017454677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
Rnor_6.01442,760,363 - 43,072,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599189   ⟹   XP_017454678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
Rnor_6.01442,760,363 - 43,072,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599190   ⟹   XP_017454679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
Rnor_6.01442,760,363 - 43,072,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091895   ⟹   XP_038947823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091896   ⟹   XP_038947824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091897   ⟹   XP_038947825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091899   ⟹   XP_038947827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091900   ⟹   XP_038947828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091901   ⟹   XP_038947829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091902   ⟹   XP_038947830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,185 (-)NCBI
RefSeq Acc Id: XM_039091903   ⟹   XP_038947831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,198,135 (-)NCBI
RefSeq Acc Id: XM_039091904   ⟹   XP_038947832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,269,390 (-)NCBI
RefSeq Acc Id: XM_039091905   ⟹   XP_038947833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,198,135 (-)NCBI
RefSeq Acc Id: XM_039091906   ⟹   XP_038947834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,198,454 (-)NCBI
RefSeq Acc Id: XM_039091907   ⟹   XP_038947835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,308,885 (-)NCBI
RefSeq Acc Id: XM_039091908   ⟹   XP_038947836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091909   ⟹   XP_038947837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091910   ⟹   XP_038947838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,425,113 (-)NCBI
RefSeq Acc Id: XM_039091911   ⟹   XP_038947839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,112,579 - 41,198,113 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178607   ⟸   NM_001191678
- UniProtKB: F1M392 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454679   ⟸   XM_017599190
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017454677   ⟸   XM_017599188
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017454678   ⟸   XM_017599189
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017454676   ⟸   XM_017599187
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: ENSRNOP00000063345   ⟸   ENSRNOT00000064263
RefSeq Acc Id: XP_038947830   ⟸   XM_039091902
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038947837   ⟸   XM_039091909
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038947838   ⟸   XM_039091910
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038947836   ⟸   XM_039091908
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038947829   ⟸   XM_039091901
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038947827   ⟸   XM_039091899
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947825   ⟸   XM_039091897
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947823   ⟸   XM_039091895
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947828   ⟸   XM_039091900
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038947824   ⟸   XM_039091896
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947835   ⟸   XM_039091907
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038947832   ⟸   XM_039091904
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038947834   ⟸   XM_039091906
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038947831   ⟸   XM_039091903
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038947833   ⟸   XM_039091905
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038947839   ⟸   XM_039091911
- Peptide Label: isoform X18
RefSeq Acc Id: ENSRNOP00000093239   ⟸   ENSRNOT00000114959
RefSeq Acc Id: ENSRNOP00000096454   ⟸   ENSRNOT00000100682
RefSeq Acc Id: ENSRNOP00000097815   ⟸   ENSRNOT00000097408
RefSeq Acc Id: ENSRNOP00000093427   ⟸   ENSRNOT00000103342
RefSeq Acc Id: ENSRNOP00000076732   ⟸   ENSRNOT00000095221
RefSeq Acc Id: ENSRNOP00000087540   ⟸   ENSRNOT00000118493
Transcriptome

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

Promoters
RGD ID:13699306
Promoter ID:EPDNEW_R9831
Type:single initiation site
Name:Limch1_1
Description:LIM and calponin homology domains 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_6.01443,072,864 - 43,072,924EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/FarMcwi (2019)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2019)
Visual CSV TAB Printer
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)
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 42606268 42606269 G C snv SHR/OlaIpcv (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 42807505 42807506 G C snv SHR/OlalpcvMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305269 AgrOrtholog
Ensembl Genes ENSRNOG00000002318 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063345 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064263 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro Calponin UniProtKB/TrEMBL
  Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  DUF4757 UniProtKB/TrEMBL
  LIMCH1 UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:305332 UniProtKB/TrEMBL
NCBI Gene 305332 ENTREZGENE
PANTHER PTHR15551:SF3 UniProtKB/TrEMBL
Pfam DUF4757 UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
  PF00307 UniProtKB/TrEMBL
PhenoGen Limch1 PhenoGen
PRINTS CALPONIN UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PS50021 UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
  SM00033 UniProtKB/TrEMBL
Superfamily-SCOP Calponin-homology UniProtKB/TrEMBL
UniProt F1M392 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Limch1  LIM and calponin homology domains 1  RGD1305269  similar to hypothetical protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305269  similar to hypothetical protein   RGD1305269_predicted  similar to hypothetical protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305269_predicted  similar to hypothetical protein (predicted)  LOC305332_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305332_predicted  similar to hypothetical protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL