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 enable protein kinase binding activity and zinc ion binding activity. Predicted to be involved in several processes, including positive regulation of cell-substrate adhesion; positive regulation of signal transduction; and regulation of gene expression. Predicted to act upstream of or within several processes, including cell-matrix adhesion; negative regulation of cell population proliferation; and negative regulation of hepatocyte apoptotic process. Part of protein-containing complex. Orthologous to human LIMS1 (LIM zinc finger domain containing 1); PARTICIPATES IN integrin mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22026,309,833 - 26,418,511 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)Ensembl
Rnor_6.02027,895,981 - 28,004,767 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)EnsemblRnor6.0rn6Rnor6.0
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


Gene-Chemical Interaction 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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. TGF-beta1 regulates the PINCH-1-integrin-linked kinase-alpha-parvin complex in glomerular cells. Jung KY, etal., J Am Soc Nephrol. 2007 Jan;18(1):66-73. Epub 2006 Dec 13.
3. TGF-beta1-induced PINCH-1-ILK-alpha-parvin complex formation regulates mesangial cell proliferation and hypertrophy. Kim SM, etal., Exp Mol Med. 2007 Aug 31;39(4):514-23.
4. ILK, PINCH and parvin: the tIPP of integrin signalling. Legate KR, etal., Nat Rev Mol Cell Biol. 2006 Jan;7(1):20-31.
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)Ensembl
Rnor_6.02027,895,981 - 28,004,767 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)EnsemblRnor6.0rn6Rnor6.0
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
GRCh382108,533,671 - 108,687,246 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2108,533,671 - 108,687,246 (+)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.02108,994,291 - 109,147,842 (+)NCBI
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
Dog10K_Boxer_Tasha1035,115,177 - 35,261,730 (-)NCBI
ROS_Cfam_1.01036,045,342 - 36,192,076 (-)NCBI
ROS_Cfam_1.0 Ensembl1036,045,345 - 36,192,039 (-)Ensembl
UMICH_Zoey_3.11035,774,284 - 35,920,701 (-)NCBI
UNSW_CanFamBas_1.01036,057,448 - 36,204,222 (-)NCBI
UU_Cfam_GSD_1.01036,249,779 - 36,396,408 (-)NCBI
Lims1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629292,157,129 - 92,210,709 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11412,059,347 - 12,210,779 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1412,059,411 - 12,213,064 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660807,500,757 - 7,651,520 (-)NCBIVero_WHO_p1.0
Lims1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474911,720,492 - 11,846,571 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Rat34  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22026,381,814 - 26,381,954 (+)MAPPERmRatBN7.2
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
mRatBN7.22026,410,405 - 26,410,555 (+)MAPPERmRatBN7.2
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
mRatBN7.22026,417,921 - 26,418,028 (+)MAPPERmRatBN7.2
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
mRatBN7.2143,435,439 - 43,435,926 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat


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_017601762 (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
mRatBN7.2 Ensembl2026,368,295 - 26,415,734 (+)Ensembl
Rnor_6.0 Ensembl2027,954,433 - 28,002,082 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092075   ⟹   ENSRNOP00000073371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,389,287 - 26,415,734 (+)Ensembl
Rnor_6.0 Ensembl2027,975,549 - 28,001,990 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094679   ⟹   ENSRNOP00000078972
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098893   ⟹   ENSRNOP00000082999
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,391,419 - 26,418,500 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101365   ⟹   ENSRNOP00000087973
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,389,287 - 26,415,536 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105423   ⟹   ENSRNOP00000080693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,393,177 - 26,415,628 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112599   ⟹   ENSRNOP00000078506
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,368,095 - 26,418,500 (+)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_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_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
RefSeq Acc Id: ENSRNOP00000078506   ⟸   ENSRNOT00000112599
RefSeq Acc Id: ENSRNOP00000080693   ⟸   ENSRNOT00000105423
RefSeq Acc Id: ENSRNOP00000082999   ⟸   ENSRNOT00000098893
RefSeq Acc Id: ENSRNOP00000078972   ⟸   ENSRNOT00000094679
RefSeq Acc Id: ENSRNOP00000087973   ⟸   ENSRNOT00000101365
Protein Domains
LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-C0KUC6-F1-model_v2 AlphaFold C0KUC6 1-387 view protein structure

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 (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
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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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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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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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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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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
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
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
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
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
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
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
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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560732 AgrOrtholog
BioCyc Gene G2FUF-3787 BioCyc
Ensembl Genes ENSRNOG00000037765 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062647 ENTREZGENE
  ENSRNOP00000062647.1 UniProtKB/TrEMBL
  ENSRNOP00000073371 ENTREZGENE
  ENSRNOP00000073371.1 UniProtKB/TrEMBL
  ENSRNOP00000078506 ENTREZGENE
  ENSRNOP00000078506.1 UniProtKB/TrEMBL
  ENSRNOP00000078972 ENTREZGENE
  ENSRNOP00000078972.1 UniProtKB/TrEMBL
  ENSRNOP00000080693.1 UniProtKB/TrEMBL
  ENSRNOP00000082999 ENTREZGENE
  ENSRNOP00000082999.1 UniProtKB/TrEMBL
  ENSRNOP00000087973 ENTREZGENE
  ENSRNOP00000087973.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064288 ENTREZGENE
  ENSRNOT00000064288.4 UniProtKB/TrEMBL
  ENSRNOT00000092075 ENTREZGENE
  ENSRNOT00000092075.2 UniProtKB/TrEMBL
  ENSRNOT00000094679 ENTREZGENE
  ENSRNOT00000094679.1 UniProtKB/TrEMBL
  ENSRNOT00000098893 ENTREZGENE
  ENSRNOT00000098893.1 UniProtKB/TrEMBL
  ENSRNOT00000101365 ENTREZGENE
  ENSRNOT00000101365.1 UniProtKB/TrEMBL
  ENSRNOT00000105423.1 UniProtKB/TrEMBL
  ENSRNOT00000112599 ENTREZGENE
  ENSRNOT00000112599.1 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
UniProt A0A8I5ZKY9_RAT UniProtKB/TrEMBL
  A0A8I5ZPU7_RAT UniProtKB/TrEMBL
  A0A8I5ZR99_RAT UniProtKB/TrEMBL
  A0A8I6A6W3_RAT UniProtKB/TrEMBL
  A0A8I6GA69_RAT UniProtKB/TrEMBL
  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