Aliases for LMTK3 Gene

Aliases for LMTK3 Gene

  • Lemur Tyrosine Kinase 3 2 3 4 5
  • TYKLM3 2 3 4
  • Protein Phosphatase 1, Regulatory Subunit 101 2 3
  • Serine/Threonine-Protein Kinase LMTK3 3 4
  • PPP1R101 2 3
  • KIAA1883 2 4
  • LMR3 2 3
  • EC 2.7.11.1 4
  • LMTK3 5

External Ids for LMTK3 Gene

Previous GeneCards Identifiers for LMTK3 Gene

  • GC19M053680
  • GC19M048988
  • GC19M045368

Summaries for LMTK3 Gene

GeneCards Summary for LMTK3 Gene

LMTK3 (Lemur Tyrosine Kinase 3) is a Protein Coding gene. Among its related pathways are Nanog in Mammalian ESC Pluripotency and Akt Signaling. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is AATK.

UniProtKB/Swiss-Prot Summary for LMTK3 Gene

  • Protein kinase which phosphorylates ESR1 (in vitro) and protects it against proteasomal degradation. May also regulate ESR1 levels indirectly via a PKC-AKT-FOXO3 pathway where it decreases the activity of PKC and the phosphorylation of AKT, thereby increasing binding of transcriptional activator FOXO3 to the ESR1 promoter and increasing ESR1 transcription (PubMed:21602804). Involved in endocytic trafficking of N-methyl-D-aspartate receptors (NMDAR) in neurons (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LMTK3 Gene

Genomics for LMTK3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LMTK3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J048513 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.1 134 1.2 SIX5 ZNF580 ZMYM3 ZNF10 POLR2A ZIC2 CHD4 ZBTB10 CEBPB ETS1 HSALNG0126878 LMTK3 lnc-LMTK3-2 CYTH2
GH19J048514 Promoter 0.8 EPDnew 250.7 +0.8 801 0.1 CEBPB PAX8 PTBP1 MLLT1 CBX1 ZNF2 ZNF664 HDAC2 SP7 ZNF18 HSALNG0126878 LMTK3 lnc-LMTK3-2 BICRA GRWD1 NOP53 SNORD35A SNRNP70 PIH1D1 NOP53-AS1
GH19J048512 Enhancer 0.7 ENCODE dbSUPER 250.7 +1.7 1656 0.2 ZNF600 SAFB RFX1 SREBF1 ZSCAN4 CREB1 POLR2A HSALNG0126878 LMTK3 lnc-LMTK3-2 HSALNG0126876 CYTH2
GH19J048283 Enhancer 0.8 Ensembl ENCODE 10.9 +229.5 229532 2 CBX1 MAFK SCRT1 ZNF184 TRIM24 KLF8 TRIM28 CBX3 CBX5 FOS ODAD1 SYNGR4 TMEM143 LMTK3 IZUMO1 GRIN2D SPHK2 lnc-ZNF114-2 piR-42491-120 ZNF114-AS1
GH19J047963 Enhancer 0.8 ENCODE 10.2 +550.6 550586 0.2 ZNF654 ZNF580 ZIC2 REST TRIM22 ZEB1 CTCF RAD21 CUX1 SMC3 BSPH1 PLA2G4C ELSPBP1 CABP5 SULT2A1 LMTK3 SYNGR4 TMEM143 SNAR-C1 piR-34822-164
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LMTK3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LMTK3

Top Transcription factor binding sites by QIAGEN in the LMTK3 gene promoter:
  • AP-4
  • c-Myc
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • Max
  • MZF-1
  • NF-Y
  • NF-YA

Genomic Locations for LMTK3 Gene

Latest Assembly
chr19:48,485,271-48,513,935
(GRCh38/hg38)
Size:
28,665 bases
Orientation:
Minus strand

Previous Assembly
chr19:48,988,528-49,016,446
(GRCh37/hg19 by Entrez Gene)
Size:
27,919 bases
Orientation:
Minus strand

chr19:48,988,528-49,016,446
(GRCh37/hg19 by Ensembl)
Size:
27,919 bases
Orientation:
Minus strand

Genomic View for LMTK3 Gene

Genes around LMTK3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMTK3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMTK3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMTK3 Gene

Proteins for LMTK3 Gene

  • Protein details for LMTK3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96Q04-LMTK3_HUMAN
    Recommended name:
    Serine/threonine-protein kinase LMTK3
    Protein Accession:
    Q96Q04
    Secondary Accessions:
    • Q4G0U1

    Protein attributes for LMTK3 Gene

    Size:
    1460 amino acids
    Molecular mass:
    153661 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with ESR1 (PubMed:21602804). Interacts with AP-2 complex subunit alpha (By similarity).
    SequenceCaution:
    • Sequence=AAH36690.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAB67776.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for LMTK3 Gene

Post-translational modifications for LMTK3 Gene

  • Glycosylation at Asn1081 and Asn1405
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LMTK3 Gene

Domains & Families for LMTK3 Gene

Gene Families for LMTK3 Gene

Protein Domains for LMTK3 Gene

Suggested Antigen Peptide Sequences for LMTK3 Gene

GenScript: Design optimal peptide antigens:
  • Lemur tyrosine kinase 3 (LMTK3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96Q04

UniProtKB/Swiss-Prot:

LMTK3_HUMAN :
  • Belongs to the protein kinase superfamily. Tyr protein kinase family.
Family:
  • Belongs to the protein kinase superfamily. Tyr protein kinase family.
genes like me logo Genes that share domains with LMTK3: view

Function for LMTK3 Gene

Molecular function for LMTK3 Gene

UniProtKB/Swiss-Prot Function:
Protein kinase which phosphorylates ESR1 (in vitro) and protects it against proteasomal degradation. May also regulate ESR1 levels indirectly via a PKC-AKT-FOXO3 pathway where it decreases the activity of PKC and the phosphorylation of AKT, thereby increasing binding of transcriptional activator FOXO3 to the ESR1 promoter and increasing ESR1 transcription (PubMed:21602804). Involved in endocytic trafficking of N-methyl-D-aspartate receptors (NMDAR) in neurons (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616, ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1; Evidence={ECO:0000269|PubMed:21602804};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060, Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013, ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216; EC=2.7.11.1; Evidence={ECO:0000269|PubMed:21602804};.

Enzyme Numbers (IUBMB) for LMTK3 Gene

Phenotypes From GWAS Catalog for LMTK3 Gene

Gene Ontology (GO) - Molecular Function for LMTK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003674 molecular_function ND --
GO:0004672 protein kinase activity IEA,IBA 21873635
GO:0004674 protein serine/threonine kinase activity IEA --
GO:0004713 protein tyrosine kinase activity IEA --
genes like me logo Genes that share ontologies with LMTK3: view
genes like me logo Genes that share phenotypes with LMTK3: view

Animal Models for LMTK3 Gene

MGI Knock Outs for LMTK3:

miRNA for LMTK3 Gene

miRTarBase miRNAs that target LMTK3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMTK3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LMTK3 Gene

Localization for LMTK3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMTK3 Gene

Membrane. Single-pass membrane protein. Cell projection, axon. Cell projection, dendrite. Golgi apparatus membrane. Note=Punctate pattern in cell projections.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMTK3 gene
Compartment Confidence
plasma membrane 3
golgi apparatus 3
extracellular 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMTK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005575 cellular_component ND --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LMTK3: view

Pathways & Interactions for LMTK3 Gene

PathCards logo

SuperPathways for LMTK3 Gene

SuperPathway Contained pathways
1 GPCR Pathway
.73
.73
.62
.59
.58
.58
.55
.38
2 ERK Signaling
.61
.61
.58
.51
.49
3 Nanog in Mammalian ESC Pluripotency
.61
.61
.59
.48
4 Actin Nucleation by ARP-WASP Complex
.66
.66
.41
5 Activation of cAMP-Dependent PKA
.77
.71
genes like me logo Genes that share pathways with LMTK3: view

Pathways by source for LMTK3 Gene

28 Qiagen pathways for LMTK3 Gene
  • 14-3-3 Induced Intracellular Signaling
  • Actin Nucleation and Branching
  • Actin Nucleation by ARP-WASP Complex
  • Activation of cAMP-Dependent PKA
  • Activation of PKA through GPCR

Interacting Proteins for LMTK3 Gene

Gene Ontology (GO) - Biological Process for LMTK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA,IBA 21873635
GO:0010923 negative regulation of phosphatase activity IDA 19389623
GO:0016310 phosphorylation IEA --
GO:0018108 peptidyl-tyrosine phosphorylation IEA --
genes like me logo Genes that share ontologies with LMTK3: view

No data available for SIGNOR curated interactions for LMTK3 Gene

Drugs & Compounds for LMTK3 Gene

(3) Drugs for LMTK3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LMTK3: view

Transcripts for LMTK3 Gene

mRNA/cDNA for LMTK3 Gene

2 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMTK3

Alternative Splicing Database (ASD) splice patterns (SP) for LMTK3 Gene

No ASD Table

Relevant External Links for LMTK3 Gene

GeneLoc Exon Structure for
LMTK3

Expression for LMTK3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LMTK3 Gene

mRNA differential expression in normal tissues according to GTEx for LMTK3 Gene

This gene is overexpressed in Brain - Cortex (x5.1), Brain - Nucleus accumbens (basal ganglia) (x5.1), Brain - Putamen (basal ganglia) (x4.6), Brain - Frontal Cortex (BA9) (x4.2), and Brain - Caudate (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for LMTK3 Gene

This gene is overexpressed in Fetal Brain (30.3), Serum (22.6), and Frontal cortex (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LMTK3 Gene



Protein tissue co-expression partners for LMTK3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LMTK3

SOURCE GeneReport for Unigene cluster for LMTK3 Gene:

Hs.207426

Evidence on tissue expression from TISSUES for LMTK3 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with LMTK3: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LMTK3 Gene

Orthologs for LMTK3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LMTK3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LMTK3 29 30
  • 96.69 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LMTK3 29 30
  • 92.07 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LMTK3 29 30
  • 91.22 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LMTK3 30
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Lmtk3 29 16 30
  • 86.94 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC691056 29
  • 86.82 (n)
Lizard
(Anolis carolinensis)
Reptilia LMTK3 30
  • 40 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lmtk3 29
  • 61.47 (n)
Zebrafish
(Danio rerio)
Actinopterygii LMTK3 30
  • 15 (a)
OneToOne
Rice
(Oryza sativa)
Liliopsida Os.46789 29
Species where no ortholog for LMTK3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LMTK3 Gene

ENSEMBL:
Gene Tree for LMTK3 (if available)
TreeFam:
Gene Tree for LMTK3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMTK3: view image
Alliance of Genome Resources:
Additional Orthologs for LMTK3

Paralogs for LMTK3 Gene

Paralogs for LMTK3 Gene

(6) SIMAP similar genes for LMTK3 Gene using alignment to 1 proteins:

  • LMTK3_HUMAN
genes like me logo Genes that share paralogs with LMTK3: view

Variants for LMTK3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LMTK3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs115496266 Benign: not provided 48,501,087(-) G/A
NM_001080434.1(LMTK3):c.1147C>T (p.Leu383=)
SYNONYMOUS
rs181429990 Benign: not provided 48,502,590(-) G/C
NM_001080434.1(LMTK3):c.733-9C>G
INTRON
rs375893711 Benign: not provided 48,491,100(-) T/G
NM_001080434.1(LMTK3):c.4453+8A>C
INTRON
rs55643178 Benign: not provided 48,501,342(-) G/T
NM_001080434.1(LMTK3):c.1029C>A (p.Leu343=)
SYNONYMOUS
rs56106717 Benign: not provided 48,502,945(-) C/T
NM_001080434.1(LMTK3):c.696G>A (p.Thr232=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LMTK3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LMTK3 Gene

Variant ID Type Subtype PubMed ID
nsv1057580 CNV gain 25217958
nsv518578 CNV loss 19592680
nsv817853 CNV loss 17921354
nsv828572 CNV loss 20364138
nsv9739 CNV gain+loss 18304495

Variation tolerance for LMTK3 Gene

Gene Damage Index Score: 2.92; 49.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMTK3 Gene

Human Gene Mutation Database (HGMD)
LMTK3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMTK3
Leiden Open Variation Database (LOVD)
LMTK3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMTK3 Gene

Disorders for LMTK3 Gene

Additional Disease Information for LMTK3

No disorders were found for LMTK3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LMTK3 Gene

Publications for LMTK3 Gene

  1. Kinome screening for regulators of the estrogen receptor identifies LMTK3 as a new therapeutic target in breast cancer. (PMID: 21602804) Giamas G … Stebbing J (Nature medicine 2011) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4
  4. Inflammation-dependent overexpression of c-Myc enhances CRL4DCAF4 E3 ligase activity and promotes ubiquitination of ST7 in colitis-associated cancer. (PMID: 30945288) Liu H … Yang C (The Journal of pathology 2019) 3
  5. LMTK3 is essential for oncogenic KIT expression in KIT-mutant GIST and melanoma. (PMID: 30242244) Klug LR … Heinrich MC (Oncogene 2019) 3

Products for LMTK3 Gene

Sources for LMTK3 Gene