Human Gene LIMK2 (uc003akk.3) Description and Page Index
  Description: Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2b, mRNA.
RefSeq Summary (NM_016733): There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. The protein encoded by this gene is phosphorylated and activated by ROCK, a downstream effector of Rho, and the encoded protein, in turn, phosphorylates cofilin, inhibiting its actin-depolymerizing activity. It is thought that this pathway contributes to Rho-induced reorganization of the actin cytoskeleton. At least three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr22:31,644,348-31,676,066 Size: 31,719 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr22:31,644,703-31,674,427 Size: 29,725 Coding Exon Count: 15 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:31,644,348-31,676,066)mRNA (may differ from genome)Protein (617 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LIMK2
CDC HuGE Published Literature: LIMK2
Positive Disease Associations: Diabetic Nephropathies
Related Studies:
  1. Diabetic Nephropathies
    Caitrin W McDonough et al. Kidney international 2011, A genome-wide association study for diabetic nephropathy genes in African Americans., Kidney international. [PubMed 21150874]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.71 RPKM in Whole Blood
Total median expression: 705.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -148.40355-0.418 Picture PostScript Text
3' UTR -613.881639-0.375 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00069 - Protein kinase domain
PF00412 - LIM domain
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF06293 - Lipopolysaccharide kinase (Kdo/WaaP) family
PF07714 - Protein tyrosine kinase

SCOP Domains:
50156 - PDZ domain-like
56112 - Protein kinase-like (PK-like)
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on P53671-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK302553 - Homo sapiens cDNA FLJ53448 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
JA482221 - Sequence 204 from Patent WO2011072091.
JE980513 - Sequence 204 from Patent EP2862929.
AK093554 - Homo sapiens cDNA FLJ36235 fis, clone THYMU2001325, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
AX748198 - Sequence 1723 from Patent EP1308459.
AK291640 - Homo sapiens cDNA FLJ76874 complete cds, highly similar to Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2a,mRNA.
D45906 - Homo sapiens mRNA for LIMK-2, complete cds.
CR456513 - Homo sapiens LIMK2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.LIMK2).
CU013400 - Homo sapiens LIMK2, mRNA (cDNA clone IMAGE:100000274), complete cds, without stop codon, in Gateway system.
CU013112 - Homo sapiens LIMK2, mRNA (cDNA clone IMAGE:100000370), complete cds, with stop codon, in Gateway system.
AB587469 - Synthetic construct DNA, clone: pF1KB8450, Homo sapiens LIMK2 gene for LIM domain kinase 2, without stop codon, in Flexi system.
AB451396 - Homo sapiens LIMK2 mRNA for LIM domain kinase 2 isoform 2a, partial cds, clone: FLJ08094AAAF.
AB451269 - Homo sapiens LIMK2 mRNA for LIM domain kinase 2 isoform 2a, complete cds, clone: FLJ08094AAAN.
AK299112 - Homo sapiens cDNA FLJ53457 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
JA482220 - Sequence 203 from Patent WO2011072091.
JE980512 - Sequence 203 from Patent EP2862929.
JA482222 - Sequence 205 from Patent WO2011072091.
JE980514 - Sequence 205 from Patent EP2862929.
AK314391 - Homo sapiens cDNA, FLJ95165, highly similar to Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2b,mRNA.
AK293774 - Homo sapiens cDNA FLJ55959 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
AL117466 - Homo sapiens mRNA; cDNA DKFZp586K0922 (from clone DKFZp586K0922).
D85527 - Homo sapiens LIMK2b mRNA, partial cds.
BC013051 - Homo sapiens LIM domain kinase 2, mRNA (cDNA clone MGC:8917 IMAGE:3861412), complete cds.
JD423629 - Sequence 404653 from Patent EP1572962.
JD086624 - Sequence 67648 from Patent EP1572962.
JD527328 - Sequence 508352 from Patent EP1572962.
KJ891550 - Synthetic construct Homo sapiens clone ccsbBroadEn_00944 LIMK2 gene, encodes complete protein.
KJ905224 - Synthetic construct Homo sapiens clone ccsbBroadEn_14690 LIMK2 gene, encodes complete protein.
AM393090 - Synthetic construct Homo sapiens clone IMAGE:100001806 for hypothetical protein (LIMK2 gene).
JD020553 - Sequence 1577 from Patent EP1572962.
JD031137 - Sequence 12161 from Patent EP1572962.
JD026097 - Sequence 7121 from Patent EP1572962.
JD032624 - Sequence 13648 from Patent EP1572962.
AK092838 - Homo sapiens cDNA FLJ35519 fis, clone SPLEN2001176.
JD420326 - Sequence 401350 from Patent EP1572962.
JD397977 - Sequence 379001 from Patent EP1572962.
JD143238 - Sequence 124262 from Patent EP1572962.
JD251131 - Sequence 232155 from Patent EP1572962.
JD313569 - Sequence 294593 from Patent EP1572962.
JD393230 - Sequence 374254 from Patent EP1572962.
JD365458 - Sequence 346482 from Patent EP1572962.
JD519780 - Sequence 500804 from Patent EP1572962.
DQ586206 - Homo sapiens piRNA piR-53318, complete sequence.
JD514354 - Sequence 495378 from Patent EP1572962.
JD362800 - Sequence 343824 from Patent EP1572962.
JD073802 - Sequence 54826 from Patent EP1572962.
JD228892 - Sequence 209916 from Patent EP1572962.
JD448876 - Sequence 429900 from Patent EP1572962.
JD165891 - Sequence 146915 from Patent EP1572962.
JD066509 - Sequence 47533 from Patent EP1572962.
JD180756 - Sequence 161780 from Patent EP1572962.
JD421767 - Sequence 402791 from Patent EP1572962.
DQ585689 - Homo sapiens piRNA piR-52801, complete sequence.
JD286482 - Sequence 267506 from Patent EP1572962.
JD246163 - Sequence 227187 from Patent EP1572962.
JD279038 - Sequence 260062 from Patent EP1572962.
JD532739 - Sequence 513763 from Patent EP1572962.
JD265539 - Sequence 246563 from Patent EP1572962.
JD415130 - Sequence 396154 from Patent EP1572962.
JD396972 - Sequence 377996 from Patent EP1572962.
DQ594610 - Homo sapiens piRNA piR-60722, complete sequence.
JD183006 - Sequence 164030 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance
hsa04666 - Fc gamma R-mediated phagocytosis
hsa04810 - Regulation of actin cytoskeleton

Reactome (by CSHL, EBI, and GO)

Protein P53671 (Reactome details) participates in the following event(s):

R-HSA-419087 LIM kinase phosphorylation by ROCK
R-HSA-3928577 ROCK phosphorylates LIMK1,2
R-HSA-3928608 LIMK phosphorylates CFL1, inactivating it
R-HSA-416572 Sema4D induced cell migration and growth-cone collapse
R-HSA-5627117 RHO GTPases Activate ROCKs
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-400685 Sema4D in semaphorin signaling
R-HSA-195258 RHO GTPase Effectors
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-373755 Semaphorin interactions
R-HSA-194315 Signaling by Rho GTPases
R-HSA-422475 Axon guidance
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: NM_016733, NP_057952, P53671-2
UCSC ID: uc003akk.3
RefSeq Accession: NM_016733
Protein: P53671-2, splice isoform of P53671 CCDS: CCDS13892.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016733.2
exon count: 15CDS single in 3' UTR: no RNA size: 3848
ORF size: 1854CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3397.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.