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 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
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 Orthologs
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
GRCr82026,851,364 - 26,961,607 (+)NCBIGRCr8
mRatBN7.22026,309,833 - 26,418,511 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2027,370,767 - 27,418,134 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02026,757,119 - 26,804,483 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02027,505,048 - 27,552,462 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
calcitriol  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP,ISO)
ethanol  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
hydrogen cyanide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
methimazole  (EXP)
paracetamol  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
poly(vinylpyrrolidone)  (EXP)
potassium cyanide  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
succimer  (ISO)
sulfadimethoxine  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)

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
GRCr82026,851,364 - 26,961,607 (+)NCBIGRCr8
mRatBN7.22026,309,833 - 26,418,511 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2027,370,767 - 27,418,134 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02026,757,119 - 26,804,483 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02027,505,048 - 27,552,462 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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.p14 Ensembl2108,533,671 - 108,687,246 (+)EnsemblGRCh38hg38GRCh38
GRCh372109,150,127 - 109,303,702 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362108,571,199 - 108,667,321 (+)NCBINCBI36Build 36hg18NCBI36
Build 342108,663,284 - 108,759,405NCBI
Celera2103,464,751 - 103,615,238 (+)NCBICelera
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 (+)NCBIT2T-CHM13v2.0
Lims1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391058,159,164 - 58,260,513 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1058,159,288 - 58,260,513 (+)EnsemblGRCm39 Ensembl
GRCm381058,323,342 - 58,424,691 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1058,323,466 - 58,424,691 (+)EnsemblGRCm38mm10GRCm38
MGSCv371057,786,295 - 57,887,437 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361057,718,904 - 57,820,046 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v21220,662,566 - 20,817,774 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A20,665,357 - 20,820,538 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A94,739,338 - 94,928,835 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A109,847,189 - 109,890,827 (+)NCBIpanpan1.1PanPan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01036,045,342 - 36,192,076 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1036,045,345 - 36,192,039 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11035,774,284 - 35,920,701 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01036,057,448 - 36,204,222 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01036,249,779 - 36,396,408 (-)NCBIUU_Cfam_GSD_1.0
Lims1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629292,157,129 - 92,210,709 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936829187,234 - 240,213 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIMS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl347,606,230 - 47,672,884 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1412,059,411 - 12,213,064 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660807,500,757 - 7,651,520 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lims1
208 total Variants
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.


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 30190.005urine total 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

Markers in Region
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


Genetic Models
This gene Lims1 is modified in the following models/strains:


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
  NM_001415155 (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_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_063279472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279474 (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
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000064288   ⟹   ENSRNOP00000062647
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,309,895 - 26,418,500 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098893   ⟹   ENSRNOP00000082999
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,391,419 - 26,418,500 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101365   ⟹   ENSRNOP00000087973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,389,287 - 26,415,536 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105423   ⟹   ENSRNOP00000080693
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2026,393,177 - 26,415,628 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112599   ⟹   ENSRNOP00000078506
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
GRCr82026,911,404 - 26,958,830 (+)NCBI
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: NM_001415155   ⟹   NP_001402084
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,853,010 - 26,961,599 (+)NCBI
mRatBN7.22026,309,896 - 26,418,503 (+)NCBI
RefSeq Acc Id: XM_006256385   ⟹   XP_006256447
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,932,356 - 26,958,813 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,932,334 - 26,961,607 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,909,001 - 26,958,813 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,851,364 - 26,958,813 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,857,400 - 26,958,813 (+)NCBI
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_017601761   ⟹   XP_017457250
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,908,995 - 26,958,813 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,910,501 - 26,961,607 (+)NCBI
mRatBN7.22026,367,395 - 26,418,511 (+)NCBI
Rnor_6.02027,952,803 - 28,004,767 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063279472   ⟹   XP_063135542
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,908,999 - 26,961,607 (+)NCBI
RefSeq Acc Id: XM_063279473   ⟹   XP_063135543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,932,363 - 26,961,607 (+)NCBI
RefSeq Acc Id: XM_063279474   ⟹   XP_063135544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82026,876,803 - 26,961,607 (+)NCBI
RefSeq Acc Id: NP_001138928   ⟸   NM_001145456
- Peptide Label: isoform 1
- UniProtKB: C0KUC5 (UniProtKB/TrEMBL),   A0A8I6GA69 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256451   ⟸   XM_006256389
- Peptide Label: isoform X6
- UniProtKB: A6K3T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256452   ⟸   XM_006256390
- Peptide Label: isoform X8
- UniProtKB: A6K3T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256450   ⟸   XM_006256388
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GA69 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256447   ⟸   XM_006256385
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A6W3 (UniProtKB/TrEMBL),   A6K3T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256449   ⟸   XM_006256387
- Peptide Label: isoform X4
- UniProtKB: C0KUC6 (UniProtKB/TrEMBL),   A6K3T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457250   ⟸   XM_017601761
- Peptide Label: isoform X1
- UniProtKB: A6K3T3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457252   ⟸   XM_017601763
- Peptide Label: isoform X3
- UniProtKB: A0A8I5ZKY9 (UniProtKB/TrEMBL),   A0A8I6GA69 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073371   ⟸   ENSRNOT00000092075
RefSeq Acc Id: ENSRNOP00000062647   ⟸   ENSRNOT00000064288
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
RefSeq Acc Id: NP_001402084   ⟸   NM_001415155
- Peptide Label: isoform 2
- UniProtKB: A0A8I6GA69 (UniProtKB/TrEMBL),   A0A8I5ZPU7 (UniProtKB/TrEMBL),   A6K3T1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135544   ⟸   XM_063279474
- Peptide Label: isoform X10
- UniProtKB: A0A8I6GA69 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135542   ⟸   XM_063279472
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063135543   ⟸   XM_063279473
- Peptide Label: isoform X9
- UniProtKB: A6K3T3 (UniProtKB/TrEMBL)
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

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 Transcript ENSRNOT00000064288 ENTREZGENE
  ENSRNOT00000064288.4 UniProtKB/TrEMBL
  ENSRNOT00000092075.2 UniProtKB/TrEMBL
  ENSRNOT00000094679 ENTREZGENE
  ENSRNOT00000094679.1 UniProtKB/TrEMBL
  ENSRNOT00000098893.1 UniProtKB/TrEMBL
  ENSRNOT00000101365.1 UniProtKB/TrEMBL
  ENSRNOT00000105423.1 UniProtKB/TrEMBL
  ENSRNOT00000112599.1 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein UniProtKB/TrEMBL
InterPro LIMS1/2-like_LIM1 UniProtKB/TrEMBL
  PINCH-1/2-like UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:499443 UniProtKB/TrEMBL
NCBI Gene 499443 ENTREZGENE
PANTHER LIM AND SENESCENT CELL ANTIGEN-LIKE-CONTAINING DOMAIN PROTEIN 1 UniProtKB/TrEMBL
  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
RatGTEx ENSRNOG00000037765 RatGTEx
SMART LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
UniProt A0A8I5ZKY9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZPU7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZR99_RAT UniProtKB/TrEMBL
  A0A8I6A6W3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GA69 ENTREZGENE, UniProtKB/TrEMBL
  A6K3T1 ENTREZGENE, UniProtKB/TrEMBL
  A6K3T3 ENTREZGENE, 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