LIMS4 (LIM zinc finger domain containing 4) - Rat Genome Database
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Gene: LIMS4 (LIM zinc finger domain containing 4) Homo sapiens
Analyze
No known orthologs.
Symbol: LIMS4
Name: LIM zinc finger domain containing 4
RGD ID: 5131296
HGNC Page HGNC
Description: Predicted to have metal ion binding activity. Predicted to localize to cytoplasm; focal adhesion; and plasma membrane; INTERACTS WITH doxorubicin.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: FLJ59124; LIM and senescent cell antigen-like domains 3-like; 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 4; LIMS3L; MGC120847; particularly interesting new Cys-His protein 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 Ensembl2110,446,640 - 110,473,075 (-)EnsemblGRCh38hg38GRCh38
GRCh382110,386,341 - 110,473,075 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372111,194,191 - 111,230,652 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2q13NCBI
HuRef2104,228,381 - 104,234,515 (-)NCBIHuRef
CHM1_12111,207,620 - 111,234,810 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
doxorubicin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15815621   PMID:25416956   PMID:32296183  


Genomics

Position Markers
RH99316  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372109,278,835 - 109,278,967UniSTSGRCh37
Build 362108,645,267 - 108,645,399RGDNCBI36
Cytogenetic Map2q12.3UniSTS
Cytogenetic Map2q13UniSTS
HuRef2102,878,847 - 102,878,979UniSTS
GeneMap99-GB4 RH Map2387.9UniSTS


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 adipose tissue appendage
High
Medium
Low 42 1010 331 9 413 19 84 39 358 157 69 370
Below cutoff 2572 2447 1444 265 653 123 4426 2510 1802 117 1102 1426 142 1560 3050

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001205288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001371340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_038099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017003103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017003104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017003105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA609556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC108938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC244199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF288404 (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

Reference Sequences
RefSeq Acc Id: ENST00000413601   ⟹   ENSP00000404432
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,465,052 - 110,473,075 (-)Ensembl
RefSeq Acc Id: ENST00000480598
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,467,914 - 110,472,934 (-)Ensembl
RefSeq Acc Id: ENST00000632758   ⟹   ENSP00000487960
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,446,640 - 110,472,860 (-)Ensembl
RefSeq Acc Id: ENST00000632897   ⟹   ENSP00000488340
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,446,739 - 110,473,041 (-)Ensembl
RefSeq Acc Id: ENST00000633364
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,465,051 - 110,472,816 (-)Ensembl
RefSeq Acc Id: NM_001205288   ⟹   NP_001192217
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,465,051 - 110,473,075 (-)NCBI
GRCh372111,194,191 - 111,230,652 (-)NCBI
CHM1_12111,226,786 - 111,234,810 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001371340   ⟹   NP_001358269
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,445,883 - 110,472,816 (-)NCBI
RefSeq Acc Id: NR_038099
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,445,883 - 110,473,075 (-)NCBI
GRCh372111,194,191 - 111,230,652 (-)NCBI
HuRef2104,228,381 - 104,234,515 (-)NCBI
CHM1_12111,207,620 - 111,234,810 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017003103   ⟹   XP_016858592
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,389,735 - 110,472,781 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017003104   ⟹   XP_016858593
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,388,848 - 110,472,781 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017003105   ⟹   XP_016858594
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,386,341 - 110,472,781 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001192217   ⟸   NM_001205288
- Peptide Label: isoform 1
- UniProtKB: P0CW20 (UniProtKB/Swiss-Prot),   P0CW19 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016858594   ⟸   XM_017003105
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_016858593   ⟸   XM_017003104
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_016858592   ⟸   XM_017003103
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001358269   ⟸   NM_001371340
- Peptide Label: isoform 2
RefSeq Acc Id: ENSP00000404432   ⟸   ENST00000413601
RefSeq Acc Id: ENSP00000488340   ⟸   ENST00000632897
RefSeq Acc Id: ENSP00000487960   ⟸   ENST00000632758
Protein Domains
LIM zinc-binding

Promoters
RGD ID:6861320
Promoter ID:EPDNEW_H3825
Type:initiation region
Name:LIMS4_1
Description:LIM zinc finger domain containing 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3826  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,472,816 - 110,472,876EPDNEW
RGD ID:6861322
Promoter ID:EPDNEW_H3826
Type:initiation region
Name:LIMS4_2
Description:LIM zinc finger domain containing 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3825  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,472,985 - 110,473,045EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q13(chr2:110104900-110611314)x3 copy number gain Autism [RCV000050514]|See cases [RCV000050514] Chr2:110104900..110611314 [GRCh38]
Chr2:110862477..111368891 [GRCh37]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:109936618-110452159)x1 copy number loss See cases [RCV000053606] Chr2:109936618..110452159 [GRCh38]
Chr2:110694195..111209736 [GRCh37]
Chr2:110051484..110644273 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110084138-110611314)x1 copy number loss See cases [RCV000053608] Chr2:110084138..110611314 [GRCh38]
Chr2:110841715..111368891 [GRCh37]
Chr2:110199004..111085360 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110104900-110611314)x3 copy number gain See cases [RCV000050514] Chr2:110104900..110611314 [GRCh38]
Chr2:110862477..111368891 [GRCh37]
Chr2:110219766..111085360 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110104900-110611314)x1 copy number loss See cases [RCV000135500] Chr2:110104900..110611314 [GRCh38]
Chr2:110862477..111368891 [GRCh37]
Chr2:110219766..111085360 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110025681-110576905)x1 copy number loss See cases [RCV000136417] Chr2:110025681..110576905 [GRCh38]
Chr2:110783258..111334482 [GRCh37]
Chr2:110140547..110811832 [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 2q13(chr2:109975055-110576905)x3 copy number gain See cases [RCV000137971] Chr2:109975055..110576905 [GRCh38]
Chr2:110732632..111334482 [GRCh37]
Chr2:110089921..110775582 [NCBI36]
Chr2:2q13
likely benign
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 2q13(chr2:110049995-110576905)x3 copy number gain See cases [RCV000138366] Chr2:110049995..110576905 [GRCh38]
Chr2:110807572..111334482 [GRCh37]
Chr2:110164861..110775582 [NCBI36]
Chr2:2q13
likely benign
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 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 2q13(chr2:110852875-111398472)x1 copy number loss See cases [RCV000598664] Chr2:110852875..111398472 [GRCh37]
Chr2:2q13
uncertain significance
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(chr2:110873834-111365996)x1 copy number loss See cases [RCV000449334] Chr2:110873834..111365996 [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 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(chr2:111186302-113273657) copy number gain Abnormality of esophagus morphology [RCV000416806] Chr2:111186302..113273657 [GRCh37]
Chr2:2q13
likely pathogenic
GRCh37/hg19 2q13(chr2:110873834-111365996)x3 copy number gain See cases [RCV000447941] Chr2:110873834..111365996 [GRCh37]
Chr2:2q13
uncertain significance
GRCh37/hg19 2q13(chr2:110874326-111365996)x1 copy number loss See cases [RCV000448315] Chr2:110874326..111365996 [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
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 2q13(chr2:110980294-113137529)x1 copy number loss not provided [RCV000682144] Chr2:110980294..113137529 [GRCh37]
Chr2:2q13
pathogenic
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
Single allele inversion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3
likely 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(chr2:110985804-111300000)x1 copy number loss not provided [RCV000740563] Chr2:110985804..111300000 [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 LIMS4 COSMIC
Ensembl Genes ENSG00000256671 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000256977 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000404432 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000405165 UniProtKB/Swiss-Prot
  ENSP00000488227 UniProtKB/Swiss-Prot
  ENSP00000488340 ENTREZGENE, UniProtKB/TrEMBL
  ENSP00000488486 UniProtKB/TrEMBL
Ensembl Transcript ENST00000413601 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000437679 UniProtKB/Swiss-Prot
  ENST00000480744 UniProtKB/TrEMBL
  ENST00000631420 UniProtKB/Swiss-Prot
  ENST00000632897 ENTREZGENE, UniProtKB/TrEMBL
GTEx ENSG00000256671 GTEx
  ENSG00000256977 GTEx
HGNC ID HGNC:39941 ENTREZGENE
Human Proteome Map LIMS4 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 100288695 ENTREZGENE
PANTHER PTHR24210 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA166049042 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
  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 LIMS4  LIM zinc finger domain containing 4    LIM-type zinc finger domains 4  Symbol and/or name change 5135510 APPROVED
2016-01-12 LIMS4  LIM-type zinc finger domains 4  LIMS3L  LIM and senescent cell antigen-like domains 3-like  Symbol and/or name change 5135510 APPROVED