Alk (ALK receptor tyrosine kinase) - Rat Genome Database

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Gene: Alk (ALK receptor tyrosine kinase) Rattus norvegicus
Analyze
Symbol: Alk
Name: ALK receptor tyrosine kinase
RGD ID: 628622
Description: Predicted to have identical protein binding activity and transmembrane receptor protein tyrosine kinase activity. Involved in nervous system development. Predicted to localize to integral component of plasma membrane and receptor complex. Orthologous to human ALK (ALK receptor tyrosine kinase); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ALK tyrosine kinase receptor; ALK tyrosine kinase receptor-like; anaplastic lymphoma kinase; anaplastic lymphoma receptor tyrosine kinase; LOC108351182
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2622,879,653 - 23,599,636 (+)NCBI
Rnor_6.0 Ensembl622,696,397 - 23,203,775 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0622,696,415 - 23,203,791 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0632,580,744 - 33,082,977 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0633,690,337 - 33,703,521 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4623,009,061 - 23,730,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1623,700,711 - 23,727,905 (+)NCBI
Celera622,414,691 - 23,129,629 (+)NCBICelera
Cytogenetic Map6q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:9174053   PMID:15886198   PMID:16880530   PMID:17487225   PMID:19056867   PMID:19200234   PMID:23382219   PMID:25326243   PMID:25517749   PMID:30497772  


Genomics

Comparative Map Data
Alk
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2622,879,653 - 23,599,636 (+)NCBI
Rnor_6.0 Ensembl622,696,397 - 23,203,775 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0622,696,415 - 23,203,791 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0632,580,744 - 33,082,977 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0633,690,337 - 33,703,521 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4623,009,061 - 23,730,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1623,700,711 - 23,727,905 (+)NCBI
Celera622,414,691 - 23,129,629 (+)NCBICelera
Cytogenetic Map6q13NCBI
ALK
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl229,192,774 - 29,921,586 (-)EnsemblGRCh38hg38GRCh38
GRCh38229,190,992 - 29,921,589 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37229,415,640 - 30,144,452 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36229,269,144 - 29,997,936 (-)NCBINCBI36hg18NCBI36
Build 34229,327,292 - 30,056,083NCBI
Celera229,260,042 - 29,988,141 (-)NCBI
Cytogenetic Map2p23.2-p23.1NCBI
HuRef229,156,646 - 29,883,927 (-)NCBIHuRef
CHM1_1229,345,879 - 30,074,503 (-)NCBICHM1_1
Alk
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391772,174,206 - 72,911,719 (-)NCBIGRCm39mm39
GRCm39 Ensembl1772,175,967 - 72,911,622 (-)Ensembl
GRCm381771,868,988 - 72,604,702 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1771,868,972 - 72,604,627 (-)EnsemblGRCm38mm10GRCm38
MGSCv371772,218,328 - 72,953,647 (-)NCBIGRCm37mm9NCBIm37
MGSCv361771,009,971 - 71,745,160 (-)NCBImm8
MGSCv361771,773,845 - 72,508,684 (-)NCBImm8
Celera1776,136,594 - 76,877,724 (-)NCBICelera
Cytogenetic Map17E1.3NCBI
cM Map1743.77NCBI
Alk
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546911,047,048 - 11,548,233 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546911,049,373 - 11,751,235 (-)NCBIChiLan1.0ChiLan1.0
ALK
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A29,276,041 - 30,007,687 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A29,276,041 - 30,006,735 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A29,196,195 - 29,930,062 (-)NCBIMhudiblu_PPA_v0panPan3
ALK
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11723,010,308 - 23,688,841 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1723,010,308 - 23,688,841 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1722,797,195 - 23,482,846 (-)NCBI
ROS_Cfam_1.01723,570,633 - 24,250,513 (-)NCBI
UMICH_Zoey_3.11722,869,939 - 23,549,638 (-)NCBI
UNSW_CanFamBas_1.01722,932,402 - 23,612,861 (-)NCBI
UU_Cfam_GSD_1.01723,038,591 - 23,719,569 (-)NCBI
Alk
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629267,167,996 - 67,810,992 (-)NCBI
SpeTri2.0NW_0049364933,624,288 - 3,671,567 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ALK
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.13109,411,146 - 110,105,755 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23116,847,214 - 116,923,998 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ALK
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11477,632,809 - 78,408,307 (+)NCBI
Alk
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473811,094,699 - 12,010,349 (-)NCBI

Position Markers
D6Rat54  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2622,959,009 - 22,959,164 (-)MAPPER
Rnor_6.0623,764,495 - 23,764,649NCBIRnor6.0
Rnor_5.0633,624,543 - 33,624,697UniSTSRnor5.0
RGSC_v3.4623,089,262 - 23,089,417RGDRGSC3.4
RGSC_v3.4623,089,263 - 23,089,417UniSTSRGSC3.4
RGSC_v3.1623,092,215 - 23,092,370RGD
Celera622,493,624 - 22,493,778UniSTS
RH 2.0 Map6192.5RGD
FHH x ACI Map620.5099RGD
Cytogenetic Map6q13UniSTS
D6Got14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,557,699 - 23,557,984 (+)MAPPER
Rnor_6.0623,164,038 - 23,164,322NCBIRnor6.0
Rnor_5.0633,043,224 - 33,043,508UniSTSRnor5.0
RGSC_v3.4623,690,605 - 23,690,890RGDRGSC3.4
RGSC_v3.4623,690,606 - 23,690,890UniSTSRGSC3.4
RGSC_v3.1623,693,558 - 23,693,843RGD
Celera623,089,298 - 23,089,582UniSTS
RH 2.0 Map6188.6RGD
Cytogenetic Map6q13UniSTS
D6Got12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,153,282 - 23,153,430 (+)MAPPER
Rnor_6.0622,757,499 - 22,757,646NCBIRnor6.0
Rnor_5.0632,642,231 - 32,642,378UniSTSRnor5.0
RGSC_v3.4623,285,110 - 23,285,258RGDRGSC3.4
RGSC_v3.4623,285,111 - 23,285,258UniSTSRGSC3.4
RGSC_v3.1623,288,063 - 23,288,211RGD
Celera622,687,007 - 22,687,154UniSTS
RH 2.0 Map6191.3RGD
Cytogenetic Map6q13UniSTS
RH131901  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,592,890 - 23,593,106 (+)MAPPER
Rnor_6.0623,198,633 - 23,198,848NCBIRnor6.0
Rnor_5.0633,077,819 - 33,078,034UniSTSRnor5.0
RGSC_v3.4623,725,781 - 23,725,996UniSTSRGSC3.4
Celera623,124,471 - 23,124,686UniSTS
Cytogenetic Map6q13UniSTS
AU048193  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,137,820 - 23,137,970 (+)MAPPER
Rnor_6.0622,742,038 - 22,742,187NCBIRnor6.0
Rnor_5.0632,626,770 - 32,626,919UniSTSRnor5.0
RGSC_v3.4623,269,650 - 23,269,799UniSTSRGSC3.4
Celera622,671,544 - 22,671,693UniSTS
Cytogenetic Map6q13UniSTS
RH136724  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,597,413 - 23,597,546 (+)MAPPER
Rnor_6.0623,203,155 - 23,203,287NCBIRnor6.0
Rnor_5.0633,082,341 - 33,082,473UniSTSRnor5.0
RGSC_v3.4623,730,303 - 23,730,435UniSTSRGSC3.4
Celera623,128,993 - 23,129,125UniSTS
Cytogenetic Map6q13UniSTS
RH138197  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2623,198,095 - 23,198,238 (+)MAPPER
Rnor_6.0622,800,737 - 22,800,879NCBIRnor6.0
Rnor_5.0632,685,469 - 32,685,611UniSTSRnor5.0
RGSC_v3.4623,329,524 - 23,329,666UniSTSRGSC3.4
Celera622,731,709 - 22,731,851UniSTS
Cytogenetic Map6q13UniSTS
AlkWKYc42g04_r1_396  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4623,316,677 - 23,316,677 (+)RGDRGSC3.4


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6123620518Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6125048718Rat
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)613505323600274Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:235
Count of miRNA genes:165
Interacting mature miRNAs:183
Transcripts:ENSRNOT00000011630
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.


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 appendage
High
Medium 11
Low 1 14 2 2 11 2 55 12 28
Below cutoff 2 21 25 12 5 12 7 7 8 14 11 11 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011630   ⟹   ENSRNOP00000011630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl622,696,397 - 23,203,775 (+)Ensembl
RefSeq Acc Id: NM_001169101   ⟹   NP_001162572
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2622,879,706 - 23,598,050 (+)NCBI
Rnor_6.0622,696,415 - 23,203,791 (+)NCBI
Rnor_5.0632,580,744 - 33,082,977 (+)NCBI
Rnor_5.0633,690,337 - 33,703,521 (-)NCBI
RGSC_v3.4623,009,061 - 23,730,939 (+)RGD
Celera622,414,691 - 23,129,629 (+)RGD
Sequence:
RefSeq Acc Id: XM_039111819   ⟹   XP_038967747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2623,350,304 - 23,599,636 (+)NCBI
RefSeq Acc Id: XR_005505446
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2622,879,653 - 23,564,923 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001162572 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967747 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAC21663 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001162572   ⟸   NM_001169101
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000011630   ⟸   ENSRNOT00000011630
RefSeq Acc Id: XP_038967747   ⟸   XM_039111819
- Peptide Label: isoform X1
Protein Domains
MAM   Protein kinase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 23009992 23009993 G T snv ACI/N (KNAW), WKY/N (KNAW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), GK/Ox (ICL), DA/BklArbNsi (ICAHN), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), WKY/NHsd (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628622 AgrOrtholog
Ensembl Genes ENSRNOG00000008683 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011630 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011630 ENTREZGENE, UniProtKB/TrEMBL
InterPro ALK UniProtKB/TrEMBL
  ConA-like_dom UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  MAM_dom UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser-Thr/Tyr-Pkinase UniProtKB/TrEMBL
  Tyr_Pkinase_cat_dom UniProtKB/TrEMBL
  Tyr_prot_kinase_AS UniProtKB/TrEMBL
  Tyr_prot_kinase_rcpt_2_CS UniProtKB/TrEMBL
NCBI Gene 266802 ENTREZGENE
PANTHER PTHR24416:SF276 UniProtKB/TrEMBL
Pfam MAM UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/TrEMBL
PhenoGen Alk PhenoGen
PRINTS TYRKINASE UniProtKB/TrEMBL
PROSITE MAM_2 UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/TrEMBL
  RECEPTOR_TYR_KIN_II UniProtKB/TrEMBL
SMART TyrKc UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
UniProt F1LRZ0_RAT UniProtKB/TrEMBL
  Q8CJH1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Alk  ALK receptor tyrosine kinase  LOC108351182  ALK tyrosine kinase receptor-like  Data Merged 737654 PROVISIONAL
2017-03-09 Alk  ALK receptor tyrosine kinase  Alk  anaplastic lymphoma receptor tyrosine kinase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-08-02 LOC108351182  ALK tyrosine kinase receptor-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-13 Alk  anaplastic lymphoma receptor tyrosine kinase  Alk  anaplastic lymphoma kinase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Alk  anaplastic lymphoma kinase      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Alk  anaplastic lymphoma kinase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease rearrangement and truncation of the human homolog occurs in some cases of non-Hodgkin lymphoma 634542