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LIMS3L Gene

protein-coding   GIFtS: 24
GCID: GC02M111204

LIM And Senescent Cell Antigen-Like Domains 3-Like

  Search for LIMS3L
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LIM And Senescent Cell Antigen-Like Domains 3-Like1 2
LIM And Senescent Cell Antigen-Like-Containing Domain Protein 3-Like2
Particularly Interesting New Cys-His Protein 32

External Ids:    HGNC: 399411   Entrez Gene: 1002886952   Ensembl: ENSG000002566717   UniProtKB: P0CW203   

Export aliases for LIMS3L gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for LIMS3L Gene:
LIMS3L (LIM and senescent cell antigen-like domains 3-like) is a protein-coding gene. An important paralog of this gene is LIMS1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for LIMS3L
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LIMS3L


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q13   Ensembl cytogenetic band:  2q13   HGNC cytogenetic band: 2q13

LIMS3L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LIMS3L gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M111204:  view genomic region     (about GC identifiers)

Start:
111,203,460 bp from pter      End:
111,230,652 bp from pter
Size:
27,193 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for LIMS3L

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LIM3L_HUMAN, P0CW20 (See protein sequence)
Recommended Name: LIM and senescent cell antigen-like-containing domain protein 3-like  
Size: 117 amino acids; 13251 Da
Secondary accessions: C9K0W2

Explore the universe of human proteins at neXtProt for LIMS3L: NX_P0CW20

REFSEQ proteins: NP_001192217.1  
ENSEMBL proteins: 
 ENSP00000404432  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR017351 PINCH
 IPR001781 Znf_LIM

Graphical View of Domain Structure for InterPro Entry P0CW20

ProtoNet protein and cluster: P0CW20

UniProtKB/Swiss-Prot: LIM3L_HUMAN, P0CW20
Similarity: Contains 1 LIM zinc-binding domain


LIMS3L for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008270zinc ion binding IEA--
     
LIMS3L for ontologies           About GeneDecksing


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hsa-miR-642a
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm ----

LIMS3L for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LIMS3L
Interactions:

    Search GeneGlobe Interaction Network for LIMS3L

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for LIMS3L (LIM3L)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for LIMS3L gene: 
NM_001205288.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000413601(uc002tfw.3) ENST00000480598
miRNA
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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LIMS3L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACCGCTTCCT
LIMS3L Expression
About this image

LIMS3L Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for LIMS3L gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves --
--
(see all 5)
Uncharacterized protein
(see all 5)


(see all 5)
many ↔ many
many ↔ many
(see all 5)
JH375335.1(7775-9525)
JH375348.1(2548-4124)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
23(a)
1 → many
3(107508842-107530508)
zebrafish
(Danio rerio)
Actinopterygii lims16
lims26
LIM and senescent cell antigen-like domains 2
15(a)
15(a)
many ↔ many
many ↔ many
11(34434877-34454717) ENSDARG00000026985
9(423983-430060) ENSDARG00000014976
fruit fly
(Drosophila melanogaster)
Insecta stck6
steamer duck
10(a)
1 → many
3R(4182689-4185686)
worm
(Caenorhabditis elegans)
Secernentea unc-976
Protein UNC-97 (unc-97) mRNA, complete cds
7(a)
1 → many
X(5593133-5594965) WBGene00006826
        Species with no ortholog for LIMS3L

ENSEMBL Gene Tree for LIMS3L (if available)
TreeFam Gene Tree for LIMS3L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for LIMS3L gene
LIMS31 2  LIMS12  PDLIM72  FHL32  FHL52  LDB32  LPXN2  FHL12  
ENSG000002572072  TGFB1I12  PDLIM52  PXN2  LIMS22  FHL22  
3 SIMAP similar genes for LIMS3L using alignment to 1 protein entry:     LIM3L_HUMAN:
LIMS3    LIMS1    LIMS2

LIMS3L for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for LIMS3L (see all 13)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1465519401,2
C--111211179(+) GTGACA/GCGATC 1 -- int10--------
rs1383399791,2
C--111211181(+) GACGCA/GATCTC 1 -- int10--------
rs2018326391,2
----111231391(+) ACAGAC/TACAAC 2 -- us2k10--------
rs2011541821,2
----111229087(+) TCTAT-/CTA   
   TCTAT
AGATA
2 -- int10--------
rs3692673721,2
----111216203(+) ATTTTC/TAGTAG 1 -- int10--------
rs2006643671,2
----111214407(+) ATTACC/TGGCAC 1 -- int10--------
rs1427972391,2
----111211141(+) GAGACA/GGAGTC 1 -- int10--------
rs2014021611,2
----111220251(+) AATGAA/TCTTGC 1 -- int10--------
rs2012707741,2
----111210781(+) TGGAGC/TGCAGT 1 -- int10--------
rs3725989131,2
----111222789(+) GATAG-/TTTTTT 2 -- ut31 int10--------

HapMap Linkage Disequilibrium report for LIMS3L (111203460 - 111230652 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for LIMS3L:    About this table    
Variant IDTypeSubtypePubMed ID
esv2751812CNV Loss17911159
nsv508157CNV Loss20534489
nsv874777CNV Gain21882294
dgv4263n71CNV Gain21882294
esv28875CNV Gain+Loss19812545
nsv469649CNV Complex16826518
nsv510884CNV Complex20534489

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for LIMS3L gene integrated from 10 sources:
(articles sorted by number of sources associating them with LIMS3L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 100288695 HGNC: 39941 Ensembl:ENSG00000256671 euGenes: HUgn100288695 ECgene: LIMS3L
H-InvDB: LIMS3L

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for LIMS3L Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for LIMS3L gene:
Search GeneIP for patents involving LIMS3L

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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