Lims1 (LIM zinc finger domain containing 1) - Rat Genome Database
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Gene: Lims1 (LIM zinc finger domain containing 1) Rattus norvegicus
Analyze
Symbol: Lims1
Name: LIM zinc finger domain containing 1
RGD ID: 1560732
Description: Predicted to have protein kinase binding activity and zinc ion binding activity. Predicted to be involved in several processes, including negative regulation of cell population proliferation; positive regulation of cell-substrate adhesion; and positive regulation of signal transduction. Localizes to protein-containing complex. Orthologous to human LIMS1 (LIM zinc finger domain containing 1); PARTICIPATES IN integrin mediated signaling pathway; INTERACTS WITH 2,6-dinitrotoluene; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LIM and senescent cell antigen-like domains 1; LIM and senescent cell antigen-like-containing domain protein 1; LIM-type zinc finger domains 1; LOC499443; Pinch1; RGD1560732; similar to LIM and senescent cell antigen-like domains 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Lims1Tn(sb-T2/Bart3)2.169Mcwi  
Genetic Models: F344-Lims1Tn(sb-T2/Bart3)2.169Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22026,309,833 - 26,418,511 (+)NCBI
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02027,895,981 - 28,004,767 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02029,715,580 - 29,824,252 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,349,188 - 37,397,427 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2027,819,971 - 27,867,155 (+)NCBICelera
Cytogenetic Map20q11NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12432066   PMID:12651156   PMID:15798193   PMID:15976450   PMID:19074270   PMID:19117955   PMID:19652092   PMID:20926685   PMID:21343177   PMID:21390327   PMID:21423176   PMID:24058607  
PMID:24719101   PMID:25931508   PMID:27771700  


Genomics

Comparative Map Data
Lims1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22026,309,833 - 26,418,511 (+)NCBI
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02027,895,981 - 28,004,767 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02029,715,580 - 29,824,252 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42037,349,188 - 37,397,427 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2027,819,971 - 27,867,155 (+)NCBICelera
Cytogenetic Map20q11NCBI
LIMS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2108,534,355 - 108,687,246 (+)EnsemblGRCh38hg38GRCh38
GRCh382108,533,671 - 108,687,246 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372109,150,127 - 109,303,702 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362108,571,199 - 108,667,321 (+)NCBINCBI36hg18NCBI36
Build 342108,663,284 - 108,759,405NCBI
Celera2103,464,751 - 103,615,238 (+)NCBI
Cytogenetic Map2q12.3NCBI
HuRef2102,803,913 - 102,903,724 (+)NCBIHuRef
CHM1_12109,154,977 - 109,307,968 (+)NCBICHM1_1
Lims1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391058,159,164 - 58,260,513 (+)NCBIGRCm39mm39
GRCm39 Ensembl1058,159,288 - 58,260,513 (+)Ensembl
GRCm381058,323,342 - 58,424,691 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1058,323,466 - 58,424,691 (+)EnsemblGRCm38mm10GRCm38
MGSCv371057,786,295 - 57,887,437 (+)NCBIGRCm37mm9NCBIm37
MGSCv361057,718,904 - 57,820,046 (+)NCBImm8
Celera1059,061,688 - 59,162,733 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1029.31NCBI
Lims1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495547012,142,997 - 12,158,273 (+)NCBIChiLan1.0ChiLan1.0
LIMS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A109,847,189 - 109,890,827 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02A94,739,338 - 94,928,835 (+)NCBIMhudiblu_PPA_v0panPan3
LIMS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11035,192,582 - 35,339,100 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lims1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936829187,234 - 240,213 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIMS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1347,607,737 - 47,704,921 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2349,748,396 - 49,812,059 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIMS1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11412,059,347 - 12,210,779 (+)NCBI
ChlSab1.1 Ensembl1412,059,411 - 12,213,064 (+)Ensembl
Lims1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474911,720,492 - 11,846,571 (+)NCBI

Position Markers
D20Rat34  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02027,968,077 - 27,968,216NCBIRnor6.0
Rnor_5.02029,787,562 - 29,787,701UniSTSRnor5.0
RGSC_v3.42037,383,774 - 37,383,914RGDRGSC3.4
RGSC_v3.42037,383,775 - 37,383,914UniSTSRGSC3.4
RGSC_v3.12037,397,574 - 37,397,714RGD
Celera2027,833,251 - 27,833,386UniSTS
SHRSP x BN Map2021.46UniSTS
SHRSP x BN Map2021.46RGD
FHH x ACI Map2012.4099RGD
Cytogenetic Map20q11UniSTS
D20Got123  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02027,996,665 - 27,996,814NCBIRnor6.0
Rnor_5.02029,816,150 - 29,816,299UniSTSRnor5.0
RGSC_v3.42037,355,177 - 37,355,326UniSTSRGSC3.4
Celera2027,861,848 - 27,861,979UniSTS
Cytogenetic Map20q11UniSTS
AW551584  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02028,004,178 - 28,004,284NCBIRnor6.0
Rnor_5.02029,823,663 - 29,823,769UniSTSRnor5.0
RGSC_v3.42037,346,894 - 37,347,000UniSTSRGSC3.4
Celera2027,869,343 - 27,869,449UniSTS
Cytogenetic Map20q11UniSTS
UniSTS:470540  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0143,726,851 - 43,727,337NCBIRnor6.0
Rnor_5.0145,056,048 - 45,056,534UniSTSRnor5.0
RGSC_v3.4137,801,439 - 37,801,925UniSTSRGSC3.4
Celera139,078,959 - 39,079,445UniSTS
Cytogenetic Map1p11UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat


Genetic Models
This gene Lims1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:696
Count of miRNA genes:264
Interacting mature miRNAs:344
Transcripts:ENSRNOT00000064288
Prediction methods:Microtar, Miranda, 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 42 46 30 19 30 8 9 74 32 35 11 8
Low 1 11 11 11 2 3 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001145456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ640984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ640985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000064288   ⟹   ENSRNOP00000062647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092075   ⟹   ENSRNOP00000073371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2027,975,549 - 28,001,990 (+)Ensembl
RefSeq Acc Id: NM_001145456   ⟹   NP_001138928
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,368,295 - 26,415,734 (+)NCBI
Rnor_6.02027,954,567 - 28,001,990 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
RGSC_v3.42037,349,188 - 37,397,427 (-)RGD
Celera2027,819,971 - 27,867,155 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256385   ⟹   XP_006256447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,389,263 - 26,415,651 (+)NCBI
Rnor_6.02027,973,727 - 28,001,858 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256387   ⟹   XP_006256449
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,389,277 - 26,418,511 (+)NCBI
Rnor_6.02027,973,730 - 28,004,767 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256388   ⟹   XP_006256450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,366,498 - 26,415,651 (+)NCBI
Rnor_6.02027,952,802 - 28,001,858 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256389   ⟹   XP_006256451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,309,833 - 26,415,651 (+)NCBI
Rnor_6.02027,895,981 - 28,001,858 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256390   ⟹   XP_006256452
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,341,925 - 26,415,651 (+)NCBI
Rnor_6.02027,926,881 - 28,001,858 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256391   ⟹   XP_006256453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,341,988 - 26,418,511 (+)NCBI
Rnor_6.02027,926,882 - 28,004,767 (+)NCBI
Rnor_5.02029,715,580 - 29,824,252 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601761   ⟹   XP_017457250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,366,489 - 26,415,651 (+)NCBI
Rnor_6.02027,952,800 - 28,001,858 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601762   ⟹   XP_017457251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02027,952,800 - 27,997,827 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601763   ⟹   XP_017457252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,367,395 - 26,418,511 (+)NCBI
Rnor_6.02027,952,803 - 28,004,767 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099025   ⟹   XP_038954953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22026,309,840 - 26,418,511 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001138928   ⟸   NM_001145456
- UniProtKB: C0KUC5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256451   ⟸   XM_006256389
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006256452   ⟸   XM_006256390
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006256453   ⟸   XM_006256391
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006256450   ⟸   XM_006256388
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006256447   ⟸   XM_006256385
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256449   ⟸   XM_006256387
- Peptide Label: isoform X4
- UniProtKB: C0KUC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457250   ⟸   XM_017601761
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457251   ⟸   XM_017601762
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457252   ⟸   XM_017601763
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000073371   ⟸   ENSRNOT00000092075
RefSeq Acc Id: ENSRNOP00000062647   ⟸   ENSRNOT00000064288
RefSeq Acc Id: XP_038954953   ⟸   XM_039099025
- Peptide Label: isoform X7
Protein Domains
LIM zinc-binding

Transcriptome

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

Promoters
RGD ID:13701585
Promoter ID:EPDNEW_R12104
Type:single initiation site
Name:Lims1_1
Description:LIM zinc finger domain containing 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_6.02027,975,566 - 27,975,626EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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
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
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/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
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 (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
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
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
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560732 AgrOrtholog
Ensembl Genes ENSRNOG00000037765 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062647 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073371 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064288 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092075 UniProtKB/TrEMBL
InterPro PINCH UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:499443 UniProtKB/TrEMBL
NCBI Gene 499443 ENTREZGENE
PANTHER PTHR24210 UniProtKB/TrEMBL
Pfam LIM UniProtKB/TrEMBL
PhenoGen Lims1 PhenoGen
PIRSF PINCH UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
Transposagen Lims1 Transposagen
UniProt C0KUC5 ENTREZGENE, UniProtKB/TrEMBL
  C0KUC6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Lims1  LIM and senescent cell antigen-like domains 1  RGD1560732_predicted  similar to LIM and senescent cell antigen-like domains 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560732_predicted  similar to LIM and senescent cell antigen-like domains 1 (predicted)  LOC499443  similar to LIM and senescent cell antigen-like domains 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499443  similar to LIM and senescent cell antigen-like domains 1      Symbol and Name status set to provisional 70820 PROVISIONAL