LIMS3 (LIM zinc finger domain containing 3) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: LIMS3 (LIM zinc finger domain containing 3) Homo sapiens
Analyze
No known orthologs.
Symbol: LIMS3
Name: LIM zinc finger domain containing 3
RGD ID: 1350402
HGNC Page HGNC
Description: Predicted to have metal ion binding activity. Predicted to localize to cytoplasm; focal adhesion; and plasma membrane; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amiodarone; arsenous acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: FLJ38851; FLJ59126; FLJ79109; LIM and senescent cell antigen-like domains 3; LIM and senescent cell antigen-like-containing domain protein 3; LIM and senescent cell antigen-like-containing domain protein 3-like; LIM and senescent cell antigen-like-containing domain protein 4; LIM-type zinc finger domains 3; LIMS3L; LIMS4; MGC138438; particularly interesting new Cys-His protein 3; pinch 2; PINCH-3
RGD Orthologs
Alliance Genes
More Info homologs ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2109,898,428 - 109,924,868 (+)EnsemblGRCh38hg38GRCh38
GRCh382109,898,688 - 109,925,625 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372110,656,009 - 110,683,202 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362110,013,558 - 110,021,322 (+)NCBINCBI36hg18NCBI36
Build 342110,657,256 - 110,665,015NCBI
Cytogenetic Map2q13NCBI
HuRef2104,228,381 - 104,234,515 (-)NCBIHuRef
CHM1_12110,676,188 - 110,690,578 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:15342556   PMID:15489334   PMID:15815621   PMID:16341674   PMID:17435276   PMID:25416956   PMID:32296183  


Genomics

Position Markers
RH98188  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372111,203,664 - 111,203,850UniSTSGRCh37
Build 362110,638,201 - 110,638,387RGDNCBI36
Cytogenetic Map2q13UniSTS
HuRef2104,228,585 - 104,228,771UniSTS
RH70783  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q12.3UniSTS
Cytogenetic Map2q13UniSTS
GeneMap99-GB4 RH Map2391.37UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:571
Count of miRNA genes:462
Interacting mature miRNAs:483
Transcripts:ENST00000437679, ENST00000482065, ENST00000487150
Prediction methods:Miranda, Rnahybrid
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 sensory system appendage entire extraembryonic component
High
Medium
Low 1 1 1 1 1 2 7 1
Below cutoff 11 2 17 6 24 8 10 11 17 29 89 25 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_033514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_027467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC013271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF288404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI887629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK096170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK298340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK300833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK312178 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK316210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC054477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC093812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC112233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC171890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM830478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP320581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ013290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX108353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF994716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000437679   ⟹   ENSP00000405165
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,898,428 - 109,906,456 (+)Ensembl
RefSeq Acc Id: ENST00000479168
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,898,670 - 109,914,635 (+)Ensembl
RefSeq Acc Id: ENST00000480744   ⟹   ENSP00000488486
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,898,729 - 109,924,769 (+)Ensembl
RefSeq Acc Id: ENST00000482065
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,898,573 - 109,903,604 (+)Ensembl
RefSeq Acc Id: ENST00000487150   ⟹   ENSP00000488782
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,901,542 - 109,906,454 (+)Ensembl
RefSeq Acc Id: ENST00000631420   ⟹   ENSP00000488227
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,898,647 - 109,924,868 (+)Ensembl
RefSeq Acc Id: NM_033514   ⟹   NP_277049
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,898,688 - 109,906,456 (+)NCBI
GRCh372110,656,009 - 110,683,202 (+)ENTREZGENE
Build 362110,013,558 - 110,021,322 (+)NCBI Archive
Sequence:
RefSeq Acc Id: NR_027467
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,898,688 - 109,925,625 (+)NCBI
GRCh372110,656,009 - 110,683,202 (+)ENTREZGENE
HuRef2104,228,381 - 104,234,515 (-)ENTREZGENE
CHM1_12110,676,188 - 110,690,578 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_277049   ⟸   NM_033514
- UniProtKB: P0CW20 (UniProtKB/Swiss-Prot),   P0CW19 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000405165   ⟸   ENST00000437679
RefSeq Acc Id: ENSP00000488486   ⟸   ENST00000480744
RefSeq Acc Id: ENSP00000488782   ⟸   ENST00000487150
RefSeq Acc Id: ENSP00000488227   ⟸   ENST00000631420
Protein Domains
LIM zinc-binding

Promoters
RGD ID:6861308
Promoter ID:EPDNEW_H3819
Type:initiation region
Name:LIMS3_2
Description:LIM zinc finger domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3820  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,898,429 - 109,898,489EPDNEW
RGD ID:6861310
Promoter ID:EPDNEW_H3820
Type:initiation region
Name:LIMS3_1
Description:LIM zinc finger domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3819  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,898,691 - 109,898,751EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3 copy number gain See cases [RCV000053141] Chr2:106696282..110223328 [GRCh38]
Chr2:107312738..110980905 [GRCh37]
Chr2:106679170..110338194 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3 copy number gain See cases [RCV000052947] Chr2:97672522..110211318 [GRCh38]
Chr2:98288985..110968895 [GRCh37]
Chr2:97655417..110326184 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q13(chr2:109623720-110207160)x1 copy number loss See cases [RCV000133772] Chr2:109623720..110207160 [GRCh38]
Chr2:110381297..110964737 [GRCh37]
Chr2:109738586..110322026 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:108719125-110611314)x3 copy number gain See cases [RCV000137361] Chr2:108719125..110611314 [GRCh38]
Chr2:109335581..111368891 [GRCh37]
Chr2:108702013..111085360 [NCBI36]
Chr2:2q13
uncertain significance
GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3 copy number gain See cases [RCV000138645] Chr2:101710825..110791418 [GRCh38]
Chr2:102327287..111548995 [GRCh37]
Chr2:101693719..111265466 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3 copy number gain See cases [RCV000139569] Chr2:106516472..110576905 [GRCh38]
Chr2:107132928..111334482 [GRCh37]
Chr2:106499360..110857227 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3 copy number gain See cases [RCV000140834] Chr2:106428663..112379067 [GRCh38]
Chr2:107045119..113136644 [GRCh37]
Chr2:106411551..112853115 [NCBI36]
Chr2:2q12.2-14.1
uncertain significance
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13
pathogenic
GRCh37/hg19 2q13(chr2:110504318-110973419)x1 copy number loss See cases [RCV000449066] Chr2:110504318..110973419 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q12.3-13(chr2:109300532-110862536)x3 copy number gain not provided [RCV000762743] Chr2:109300532..110862536 [GRCh37]
Chr2:2q12.3-13
uncertain significance
Single allele duplication Autism spectrum disorder [RCV000208724] Chr2:109696399..110327308 [GRCh38]
Chr2:110453976..111084885 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q12.2-14.1(chr2:106423310-115054828)x1 copy number loss See cases [RCV000240053] Chr2:106423310..115054828 [GRCh37]
Chr2:2q12.2-14.1
pathogenic
GRCh37/hg19 2q12.3-14.3(chr2:109798247-125658380)x1 copy number loss See cases [RCV000240485] Chr2:109798247..125658380 [GRCh37]
Chr2:2q12.3-14.3
pathogenic
GRCh37/hg19 2q12.3-14.1(chr2:109556627-117570152)x1 copy number loss See cases [RCV000240490] Chr2:109556627..117570152 [GRCh37]
Chr2:2q12.3-14.1
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q13(chr2:110504318-110983418)x1 copy number loss See cases [RCV000446820] Chr2:110504318..110983418 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q11.1-13(chr2:95327499-111370025)x4 copy number gain See cases [RCV000446842] Chr2:95327499..111370025 [GRCh37]
Chr2:2q11.1-13
pathogenic
GRCh37/hg19 2q12.3-13(chr2:108526025-110876776)x3 copy number gain See cases [RCV000446992] Chr2:108526025..110876776 [GRCh37]
Chr2:2q12.3-13
uncertain significance
GRCh37/hg19 2q13(chr2:110496601-110983418)x3 copy number gain See cases [RCV000446128] Chr2:110496601..110983418 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q13(chr2:110497990-111400649)x3 copy number gain See cases [RCV000447601] Chr2:110497990..111400649 [GRCh37]
Chr2:2q13
likely benign
GRCh37/hg19 2q13(chr2:110504318-111365996)x1 copy number loss See cases [RCV000445912] Chr2:110504318..111365996 [GRCh37]
Chr2:2q13
conflicting data from submitters
GRCh37/hg19 2q13(chr2:110504318-111370025)x3 copy number gain See cases [RCV000446018] Chr2:110504318..111370025 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q13(chr2:110504318-110980108)x1 copy number loss See cases [RCV000448720] Chr2:110504318..110980108 [GRCh37]
Chr2:2q13
likely pathogenic
GRCh37/hg19 2q13(chr2:110498141-110983418)x3 copy number gain See cases [RCV000448038] Chr2:110498141..110983418 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q13(chr2:110504318-111365996)x3 copy number gain See cases [RCV000448330] Chr2:110504318..111365996 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
Single allele inversion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3
likely pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q12.1-24.3(chr2:104172062-168223828)x1 copy number loss PARP Inhibitor response [RCV000626436] Chr2:104172062..168223828 [GRCh37]
Chr2:2q12.1-24.3
drug response
Single allele duplication not provided [RCV000678012] Chr2:107096423..112235727 [GRCh37]
Chr2:2q12.2-13
likely pathogenic
GRCh37/hg19 2q13(chr2:110504318-111622976)x3 copy number gain not provided [RCV000682117] Chr2:110504318..111622976 [GRCh37]
Chr2:2q13
likely benign
GRCh37/hg19 2q12.2-13(chr2:107020782-111365996)x1 copy number loss not provided [RCV000682152] Chr2:107020782..111365996 [GRCh37]
Chr2:2q12.2-13
likely pathogenic
GRCh37/hg19 2q11.1-13(chr2:96353030-114045463)x3 copy number gain not provided [RCV000682168] Chr2:96353030..114045463 [GRCh37]
Chr2:2q11.1-13
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q13(chr2:110508213-110749788)x1 copy number loss not provided [RCV000753080] Chr2:110508213..110749788 [GRCh37]
Chr2:2q13
benign
GRCh37/hg19 2q12.2-13(chr2:107029680-113187742)x1 copy number loss not provided [RCV001259645] Chr2:107029680..113187742 [GRCh37]
Chr2:2q12.2-13
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LIMS3 COSMIC
Ensembl Genes ENSG00000256671 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000256977 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000404432 UniProtKB/Swiss-Prot
  ENSP00000405165 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000488227 UniProtKB/Swiss-Prot
  ENSP00000488340 UniProtKB/TrEMBL
  ENSP00000488486 UniProtKB/TrEMBL
  ENSP00000488782 UniProtKB/TrEMBL
Ensembl Transcript ENST00000413601 UniProtKB/Swiss-Prot
  ENST00000437679 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000480744 UniProtKB/TrEMBL
  ENST00000487150 UniProtKB/TrEMBL
  ENST00000631420 UniProtKB/Swiss-Prot
  ENST00000632897 UniProtKB/TrEMBL
GTEx ENSG00000256671 GTEx
  ENSG00000256977 GTEx
HGNC ID HGNC:30047 ENTREZGENE
Human Proteome Map LIMS3 Human Proteome Map
InterPro PINCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:100288695 UniProtKB/Swiss-Prot
  hsa:96626 UniProtKB/Swiss-Prot
NCBI Gene 96626 ENTREZGENE
PANTHER PTHR24210 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134917873 PharmGKB
PIRSF PINCH UniProtKB/TrEMBL
PROSITE LIM_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Hs.535619 ENTREZGENE
  Hs.735995 ENTREZGENE
UniProt A0A0J9YXC7_HUMAN UniProtKB/TrEMBL
  A0A0J9YYC1_HUMAN UniProtKB/TrEMBL
  LIMS3_HUMAN UniProtKB/Swiss-Prot
  LIMS4_HUMAN UniProtKB/Swiss-Prot
  P0CW19 ENTREZGENE
  P0CW20 ENTREZGENE
UniProt Secondary A0A0A6YYD2 UniProtKB/Swiss-Prot
  B4DPH6 UniProtKB/Swiss-Prot
  C9K0W2 UniProtKB/Swiss-Prot
  Q9HB10 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-16 LIMS3  LIM zinc finger domain containing 3    LIM-type zinc finger domains 3  Symbol and/or name change 5135510 APPROVED
2016-01-12 LIMS3  LIM-type zinc finger domains 3    LIM and senescent cell antigen-like domains 3  Symbol and/or name change 5135510 APPROVED