Lims1 (LIM zinc finger domain containing 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Lims1 (LIM zinc finger domain containing 1) Heterocephalus glaber
Analyze
Symbol: Lims1
Name: LIM zinc finger domain containing 1
RGD ID: 18933406
Description: ENCODES a protein that exhibits protein kinase binding (ortholog); protein-containing complex binding (ortholog); zinc ion binding (ortholog); INVOLVED IN cell-cell adhesion (ortholog); cell-cell junction organization (ortholog); cell-matrix adhesion (ortholog); PARTICIPATES IN integrin mediated signaling pathway; ASSOCIATED WITH autosomal dominant distal hereditary motor neuronopathy 7 (ortholog); ectodermal dysplasia 10A (ortholog); ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED, SUSCEPTIBILITY TO, 3 (ortholog); FOUND IN perinuclear region of cytoplasm (ortholog); protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LIM and senescent cell antigen-like-containing domain protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474911,720,492 - 11,846,571 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:21993625   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
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
(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
(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


Expression


Sequence


Reference Sequences
RefSeq Acc Id: XM_004844508   ⟹   XP_004844565
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474911,797,590 - 11,846,571 (+)NCBI
RefSeq Acc Id: XM_004844509   ⟹   XP_004844566
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474911,797,599 - 11,846,571 (+)NCBI
RefSeq Acc Id: XM_004844510   ⟹   XP_004844567
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474911,797,606 - 11,846,571 (+)NCBI
RefSeq Acc Id: XM_021258154   ⟹   XP_021113813
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474911,797,590 - 11,846,571 (+)NCBI
RefSeq Acc Id: XM_021258155   ⟹   XP_021113814
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474911,720,492 - 11,846,571 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_021113814   ⟸   XM_021258155
- Peptide Label: isoform X5
RefSeq Acc Id: XP_021113813   ⟸   XM_021258154
- Peptide Label: isoform X1
RefSeq Acc Id: XP_004844565   ⟸   XM_004844508
- Peptide Label: isoform X2
RefSeq Acc Id: XP_004844566   ⟸   XM_004844509
- Peptide Label: isoform X3
RefSeq Acc Id: XP_004844567   ⟸   XM_004844510
- Peptide Label: isoform X4
- UniProtKB: G5CB91 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000013204 ENTREZGENE
  ENSHGLG00000049144 UniProtKB/TrEMBL
  ENSHGLG00100010906 UniProtKB/TrEMBL
Ensembl Transcript ENSHGLT00000018605 ENTREZGENE
  ENSHGLT00000018606 ENTREZGENE
  ENSHGLT00000018607 ENTREZGENE
  ENSHGLT00000054237 UniProtKB/TrEMBL
  ENSHGLT00100063450 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
NCBI Gene Lims1 ENTREZGENE
PANTHER LIM AND SENESCENT CELL ANTIGEN-LIKE-CONTAINING DOMAIN PROTEIN 1 UniProtKB/TrEMBL
  PTHR24210 UniProtKB/TrEMBL
Pfam LIM UniProtKB/TrEMBL
PIRSF PINCH UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
UniProt G5CB91 ENTREZGENE, UniProtKB/TrEMBL