Lck (LCK proto-oncogene, Src family tyrosine kinase) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Lck (LCK proto-oncogene, Src family tyrosine kinase) Rattus norvegicus
Analyze
Symbol: Lck
Name: LCK proto-oncogene, Src family tyrosine kinase
RGD ID: 2994
Description: Enables antigen binding activity and protein tyrosine kinase activity. Involved in several processes, including positive regulation of uterine smooth muscle contraction; protein phosphorylation; and response to aldosterone. Located in endocytic vesicle. Is active in glutamatergic synapse and postsynaptic specialization, intracellular component. Used to study allergic conjunctivitis and human immunodeficiency virus infectious disease. Biomarker of retinal degeneration. Human ortholog(s) of this gene implicated in immunodeficiency 22. Orthologous to human LCK (LCK proto-oncogene, Src family tyrosine kinase); PARTICIPATES IN eicosanoid signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; glypican signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; 7,12-dimethyltetraphene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Lck1; Lck_mapped; Lcktkr; lymphocyte cell-specific protein-tyrosine kinase; lymphocyte protein tyrosine kinase; lymphocyte protein tyrosine kinase (mapped); lymphocyte-specific protein tyrosine kinase; p56-LCK; proto-oncogene tyrosine-protein kinase LCK
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,172,642 - 147,201,267 (-)NCBIGRCr8
mRatBN7.25141,888,318 - 141,916,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5141,888,326 - 141,903,794 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5144,589,698 - 144,600,304 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05146,359,523 - 146,370,129 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05146,356,103 - 146,366,907 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05147,750,976 - 147,779,627 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5147,750,973 - 147,761,983 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05151,480,214 - 151,509,064 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,707,505 - 148,718,296 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5140,363,592 - 140,374,224 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R,R,R)-alpha-tocopherol  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acetohydrazide  (ISO)
acetylsalicylic acid  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
alpha-Zearalanol  (EXP)
alsterpaullone  (ISO)
amosite asbestos  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arotinoid acid  (ISO)
Atractylone  (EXP)
benzo[a]pyrene  (ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
CHIR 99021  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
compound 48/80  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
cortisol  (ISO)
crizotinib  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
dexamethasone  (ISO)
Dibutyl phosphate  (ISO)
diethylstilbestrol  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
enzalutamide  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
glutathione  (ISO)
hydrazine  (ISO)
hydroxychloroquine  (ISO)
indirubin-3'-monoxime  (ISO)
isotretinoin  (ISO)
kenpaullone  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
lead diacetate  (ISO)
manganese(II) chloride  (ISO)
methotrexate  (ISO)
methoxyacetic acid  (EXP)
methylmercury chloride  (ISO)
N,O-dimethyltyramine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
nicotine  (ISO)
oxaliplatin  (EXP)
oxybenzone  (ISO)
ozone  (ISO)
paracetamol  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
ponatinib  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
protein kinase inhibitor  (ISO)
pyrazoles  (ISO)
pyrimidines  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenic acid  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sorafenib  (ISO)
SU6656  (ISO)
succimer  (ISO)
sulfasalazine  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
teriflunomide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
XAV939  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
B cell receptor signaling pathway  (IBA,ISO)
CD27 signaling pathway  (IEA,ISO)
cell surface receptor protein tyrosine kinase signaling pathway  (IBA)
cell surface receptor signaling pathway  (ISO)
Fc-gamma receptor signaling pathway  (IEA,ISO)
gamma-delta T cell differentiation  (ISO)
innate immune response  (IBA)
intracellular signal transduction  (IEA,ISO)
intracellular zinc ion homeostasis  (IEA,ISO)
peptidyl-tyrosine autophosphorylation  (IEA,ISO)
peptidyl-tyrosine phosphorylation  (IDA,ISO)
positive regulation of gamma-delta T cell differentiation  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of heterotypic cell-cell adhesion  (IEA,ISO)
positive regulation of intrinsic apoptotic signaling pathway  (IEA,ISO)
positive regulation of leukocyte cell-cell adhesion  (ISO)
positive regulation of T cell activation  (IEA,ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (ISO)
positive regulation of uterine smooth muscle contraction  (IMP)
protein autophosphorylation  (IDA,ISO)
protein phosphorylation  (IEA,ISO)
regulation of regulatory T cell differentiation  (ISO)
regulation of T cell receptor signaling pathway  (ISO)
release of sequestered calcium ion into cytosol  (ISO)
response to aldosterone  (IEP)
response to hydrogen peroxide  (IDA)
response to mechanical stimulus  (IMP)
response to metal ion  (IDA)
response to xenobiotic stimulus  (IEA,ISO)
response to zinc ion  (IEP)
T cell activation  (ISO)
T cell differentiation  (IBA,IEA,ISO)
T cell receptor signaling pathway  (IEA,ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Ag-specific recognition, activation, and effector function of T cells in the conjunctiva with experimental immune-mediated blepharoconjunctivitis. Fukushima A, etal., Invest Ophthalmol Vis Sci. 2003 Oct;44(10):4366-74.
2. Cellular depletion of p56lck during thymocyte apoptosis. Garcia-Welsh A, etal., J Leukoc Biol. 1994 Oct;56(4):528-32.
3. The association of the protein tyrosine kinases p56lck and p60fyn with the glycosyl phosphatidylinositol-anchored proteins Thy-1 and CD48 in rat thymocytes is dependent on the state of cellular activation. Garnett D, etal., Eur J Immunol. 1993 Oct;23(10):2540-4.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. The activated form of the Lck tyrosine protein kinase in cells exposed to hydrogen peroxide is phosphorylated at both Tyr-394 and Tyr-505. Hardwick JS and Sefton BM, J Biol Chem. 1997 Oct 10;272(41):25429-32.
6. Age-related changes in p56lck protein levels and phenotypic distribution of T lymphocytes in young rats. Hosea HJ, etal., Clin Dev Immunol. 2005 Mar;12(1):75-84.
7. Zinc-deficient rats have fewer recent thymic emigrant (CD90+) T lymphocytes in spleen and blood. Hosea HJ, etal., J Nutr. 2003 Dec;133(12):4239-42.
8. Interactions between Src family protein tyrosine kinases and PSD-95. Kalia LV and Salter MW, Neuropharmacology. 2003 Nov;45(6):720-8.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Protein interactions between CD2 and Lck are required for the lipid raft distribution of CD2. Nunes RJ, etal., J Immunol. 2008 Jan 15;180(2):988-97.
11. Gene expression changes in the retina after systemic administration of aldosterone. Ono A, etal., Jpn J Ophthalmol. 2018 Jul;62(4):499-507. doi: 10.1007/s10384-018-0595-4. Epub 2018 Apr 30.
12. Assembly of the CD8alpha/p56(lck) protein complex in stably expressing rat epithelial cells. Pascale MC, etal., FEBS Lett. 2000 Sep 1;480(2-3):226-30.
13. Role of nonreceptor protein tyrosine kinases during phospholipase C-gamma 1-related uterine contractions in the rat. Phillippe M, etal., Reprod Sci. 2009 Mar;16(3):265-73.
14. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
15. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. PKC-interacting proteins: from function to pharmacology. Poole AW, etal., Trends Pharmacol Sci. 2004 Oct;25(10):528-35.
17. GOA pipeline RGD automated data pipeline
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Gold is a T cell polyclonal activator in BN and LEW rats but favors IL-4 expression only in autoimmune prone BN rats. Savignac M, etal., Eur J Immunol. 2001 Aug;31(8):2266-76.
20. The Src family kinases, Fgr, Fyn, Lck, and Lyn, colocalize with coated membranes in platelets. Stenberg PE, etal., Blood. 1997 Apr 1;89(7):2384-93.
21. A therapeutic anti-CD4 monoclonal antibody inhibits T cell receptor signal transduction in mouse autoimmune cardiomyopathy. Wang ZH, etal., Chin Med J (Engl). 2007 Aug 5;120(15):1319-25.
22. HIV-1 transgenic rat CD4+ T cells develop decreased CD28 responsiveness and suboptimal Lck tyrosine dephosphorylation following activation. Yadav A, etal., Virology. 2006 Sep 30;353(2):357-65. Epub 2006 Jul 10.
23. Lck is required for activation-induced T cell death after TCR ligation with partial agonists. Yu XZ, etal., J Immunol 2004 Feb 1;172(3):1437-43.
Additional References at PubMed
PMID:214242   PMID:1381360   PMID:1505025   PMID:1579166   PMID:2470098   PMID:3262426   PMID:7486703   PMID:7499277   PMID:7504174   PMID:7513706   PMID:7807014   PMID:7852312  
PMID:8175795   PMID:8423992   PMID:8506364   PMID:8618896   PMID:8681956   PMID:8761480   PMID:8794306   PMID:8943371   PMID:9169414   PMID:9177270   PMID:9799234   PMID:11254359  
PMID:11739864   PMID:12150984   PMID:12477932   PMID:12732664   PMID:12923167   PMID:14752163   PMID:15671290   PMID:16116473   PMID:16245368   PMID:16709819   PMID:17118402   PMID:18697750  
PMID:20007709   PMID:20458337   PMID:20624904   PMID:21245484   PMID:21357543   PMID:21487392   PMID:22080863   PMID:22828953   PMID:23376485   PMID:23715271   PMID:23793062   PMID:24463463  
PMID:24714587   PMID:27400149   PMID:38263783  


Genomics

Comparative Map Data
Lck
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,172,642 - 147,201,267 (-)NCBIGRCr8
mRatBN7.25141,888,318 - 141,916,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5141,888,326 - 141,903,794 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5144,589,698 - 144,600,304 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05146,359,523 - 146,370,129 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05146,356,103 - 146,366,907 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05147,750,976 - 147,779,627 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5147,750,973 - 147,761,983 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05151,480,214 - 151,509,064 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,707,505 - 148,718,296 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5140,363,592 - 140,374,224 (-)NCBICelera
Cytogenetic Map5q36NCBI
LCK
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38132,251,265 - 32,286,165 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl132,251,244 - 32,286,165 (+)EnsemblGRCh38hg38GRCh38
GRCh37132,716,866 - 32,751,766 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36132,489,427 - 32,524,353 (+)NCBINCBI36Build 36hg18NCBI36
Build 34132,386,024 - 32,420,854NCBI
Celera130,987,010 - 31,022,233 (+)NCBICelera
Cytogenetic Map1p35.2NCBI
HuRef130,833,080 - 30,867,241 (+)NCBIHuRef
CHM1_1132,832,435 - 32,867,211 (+)NCBICHM1_1
T2T-CHM13v2.0132,109,169 - 32,144,081 (+)NCBIT2T-CHM13v2.0
Lck
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394129,442,142 - 129,467,415 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4129,442,137 - 129,467,434 (-)EnsemblGRCm39 Ensembl
GRCm384129,548,344 - 129,573,641 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4129,548,344 - 129,573,641 (-)EnsemblGRCm38mm10GRCm38
MGSCv374129,225,588 - 129,250,885 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364129,050,662 - 129,060,676 (-)NCBIMGSCv36mm8
Celera4127,881,707 - 127,907,449 (-)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map463.26NCBI
Lck
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545210,608,318 - 10,632,310 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545210,608,317 - 10,632,310 (+)NCBIChiLan1.0ChiLan1.0
LCK
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21194,540,879 - 194,576,384 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11193,662,224 - 193,697,739 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0131,560,229 - 31,572,391 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1132,567,712 - 32,579,923 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl132,565,739 - 32,579,923 (+)Ensemblpanpan1.1panPan2
LCK
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,940,816 - 68,964,585 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,941,249 - 68,964,567 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha265,521,599 - 65,545,402 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0269,507,326 - 69,531,453 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl269,507,329 - 69,531,404 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1266,344,251 - 66,368,026 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0267,339,915 - 67,363,766 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0268,338,870 - 68,362,999 (-)NCBIUU_Cfam_GSD_1.0
Lck
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505849,480,227 - 49,489,329 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647415,305,050 - 15,313,668 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647415,293,115 - 15,314,072 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCK
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl688,720,176 - 88,745,914 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1688,719,886 - 88,745,922 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2682,843,255 - 82,852,667 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCK
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120100,582,718 - 100,618,041 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603316,070,565 - 16,104,978 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lck
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476415,472,685 - 15,495,351 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476415,469,582 - 15,495,351 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lck
171 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:274
Count of miRNA genes:174
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000012936
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat

Markers in Region
D5Wox15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,899,404 - 141,899,523 (+)MAPPERmRatBN7.2
Rnor_6.05147,762,065 - 147,762,183NCBIRnor6.0
Rnor_5.05151,491,781 - 151,491,899UniSTSRnor5.0
RGSC_v3.45148,718,587 - 148,718,705UniSTSRGSC3.4
Celera5140,374,515 - 140,374,633UniSTS
Cytogenetic Map5q36UniSTS
RH132104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,888,369 - 141,888,574 (+)MAPPERmRatBN7.2
Rnor_6.05147,751,029 - 147,751,233NCBIRnor6.0
Rnor_5.05151,480,267 - 151,480,471UniSTSRnor5.0
RGSC_v3.45148,707,551 - 148,707,755UniSTSRGSC3.4
Celera5140,363,638 - 140,363,842UniSTS
RH 3.4 Map5959.81UniSTS
Cytogenetic Map5q36UniSTS
PMC166405P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,897,632 - 141,897,996 (+)MAPPERmRatBN7.2
Rnor_6.05147,760,291 - 147,760,656NCBIRnor6.0
Rnor_5.05151,490,008 - 151,490,373UniSTSRnor5.0
RGSC_v3.45148,716,813 - 148,717,178UniSTSRGSC3.4
Celera5140,372,745 - 140,373,110UniSTS
Cytogenetic Map5q36UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000012936   ⟹   ENSRNOP00000012936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5141,888,326 - 141,903,794 (-)Ensembl
Rnor_6.0 Ensembl5147,750,973 - 147,761,983 (-)Ensembl
RefSeq Acc Id: NM_001100709   ⟹   NP_001094179
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85147,172,642 - 147,183,650 (-)NCBI
mRatBN7.25141,888,318 - 141,899,325 (-)NCBI
Rnor_6.05147,750,983 - 147,761,774 (-)NCBI
Rnor_5.05151,480,214 - 151,509,064 (-)NCBI
RGSC_v3.45148,707,505 - 148,718,296 (-)RGD
Celera5140,363,592 - 140,374,224 (-)RGD
Sequence:
RefSeq Acc Id: NM_001415870   ⟹   NP_001402799
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85147,172,642 - 147,201,267 (-)NCBI
mRatBN7.25141,888,318 - 141,916,945 (-)NCBI
RefSeq Acc Id: XM_006238932   ⟹   XP_006238994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85147,172,648 - 147,183,671 (-)NCBI
mRatBN7.25141,888,319 - 141,899,360 (-)NCBI
Rnor_6.05147,750,976 - 147,762,038 (-)NCBI
Rnor_5.05151,480,214 - 151,509,064 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001094179   ⟸   NM_001100709
- UniProtKB: Q01621 (UniProtKB/Swiss-Prot),   B1H265 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006238994   ⟸   XM_006238932
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHH7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012936   ⟸   ENSRNOT00000012936
RefSeq Acc Id: NP_001402799   ⟸   NM_001415870
- UniProtKB: Q01621 (UniProtKB/Swiss-Prot),   B1H265 (UniProtKB/Swiss-Prot)
Protein Domains
Protein kinase   SH2   SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q01621-F1-model_v2 AlphaFold Q01621 1-509 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694069
Promoter ID:EPDNEW_R4593
Type:multiple initiation site
Name:Lck_1
Description:LCK proto-oncogene, Src family tyrosine kinase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05147,761,974 - 147,762,034EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2994 AgrOrtholog
BioCyc Gene G2FUF-39791 BioCyc
Ensembl Genes ENSRNOG00000009705 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012936.7 UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 Domains UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transferase(Phosphotransferase) domain 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7381544 IMAGE-MGC_LOAD
  IMAGE:7384919 IMAGE-MGC_LOAD
InterPro Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lck_SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lck_SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Non-receptor_tyrosine_kinases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:313050 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116394 IMAGE-MGC_LOAD
  MGC:188286 IMAGE-MGC_LOAD
NCBI Gene Lck ENTREZGENE
PANTHER TYROSINE-PROTEIN KINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYROSINE-PROTEIN KINASE LCK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Pkinase_Tyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB LCK RGD
PhenoGen Lck PhenoGen
PRINTS SH2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYRKINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009705 RatGTEx
SMART SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TyrKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55550 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHH7 ENTREZGENE, UniProtKB/TrEMBL
  B1H265 ENTREZGENE
  LCK_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4FZR6_RAT UniProtKB/TrEMBL
UniProt Secondary B1H265 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Lck  LCK proto-oncogene, Src family tyrosine kinase  Lck  lymphocyte-specific protein tyrosine kinase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-17 Lck  lymphocyte-specific protein tyrosine kinase  Lck  lymphocyte protein tyrosine kinase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-03-14 Lck  lymphocyte protein tyrosine kinase  Lck_predicted  lymphocyte protein tyrosine kinase (predicted)  Symbol and Name updated 1299863 APPROVED
2007-03-05 Lck_predicted  lymphocyte protein tyrosine kinase (predicted)  Lck_mapped  lymphocyte protein tyrosine kinase (mapped)  Symbol and Name updated 1299863 APPROVED
2007-03-05 Lck_mapped  lymphocyte protein tyrosine kinase (mapped)  Lck_retired    Data merged from RGD:1586168 737654 APPROVED
2006-11-19 Lck  lymphocyte protein tyrosine kinase (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Lck_mapped  lymphocyte protein tyrosine kinase (mapped)      Symbol and Name updated 1556543 APPROVED
2002-06-10 Lck  Lymphocyte-specific protein tyrosine kinase      Symbol and Name status set to approved 70586 APPROVED