Lamp1 (lysosomal-associated membrane protein 1) - Rat Genome Database

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Gene: Lamp1 (lysosomal-associated membrane protein 1) Rattus norvegicus
Analyze
Symbol: Lamp1
Name: lysosomal-associated membrane protein 1
RGD ID: 2989
Description: Predicted to enable enzyme binding activity and protein domain specific binding activity. Involved in autophagic cell death. Located in several cellular components, including cytoplasmic vesicle; lysosome; and neuronal cell body. Is integral component of synaptic vesicle membrane. Orthologous to human LAMP1 (lysosomal associated membrane protein 1); PARTICIPATES IN autophagy pathway; phagocytosis pathway; tuberculosis pathway; INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 120 kDa lysosomal membrane glycoprotein; CD107 antigen-like family member A; LAMP-1; LGP-120; LGP120; Lysosomal associated membrane protein 1 (120 kDa); lysosomal membrane glycoprotein 1; lysosome-associated membrane glycoprotein 1; lysosome-associated membrane protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21676,355,982 - 76,380,700 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1676,355,984 - 76,381,883 (-)Ensembl
Rnor_6.01681,689,576 - 81,714,341 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,689,335 - 81,714,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,175,574 - 81,200,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,213,165 - 81,230,019 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11681,213,425 - 81,230,284 (-)NCBI
Celera1674,162,536 - 74,179,021 (-)NCBICelera
RH 3.4 Map16744.4RGD
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
3',5'-cyclic AMP  (EXP)
3-chloropropane-1,2-diol  (ISO)
3-methyladenine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
aconitine  (EXP)
acrolein  (EXP)
acrylamide  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
biotin  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
captan  (ISO)
carbon disulfide  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
chloropicrin  (ISO)
cholesterol  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
coumestrol  (ISO)
Cuprizon  (ISO)
curcumin  (EXP)
D-glucose  (EXP)
decabromodiphenyl ether  (EXP)
deguelin  (ISO)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ferric oxide  (EXP)
flunarizine  (EXP)
flusilazole  (EXP)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
genistein  (ISO)
glucose  (EXP)
ionomycin  (ISO)
isoniazide  (ISO)
ivermectin  (ISO)
lead nitrate  (ISO)
lipopolysaccharide  (ISO)
methamphetamine  (ISO)
methyl methanesulfonate  (ISO)
Methylazoxymethanol acetate  (EXP)
Mibefradil  (EXP)
microcystin-LR  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
oligomycin A  (ISO)
paraquat  (ISO)
phenobarbital  (EXP)
phenylpropanolamine  (ISO)
phosphoramide mustard  (EXP)
picoxystrobin  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
pyrroloquinoline quinone  (ISO)
resveratrol  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
taurine  (ISO)
tebufenpyrad  (ISO)
temozolomide  (ISO)
thapsigargin  (EXP)
trichloroethene  (EXP)
trifluoperazine  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
Xanthatin  (ISO)
Yessotoxin  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Adams LD, etal., Arterioscler Thromb Vasc Biol 1999 Nov;19(11):2600-8.
2. Elhaik-Goldman S, etal., PLoS One. 2011;6(8):e23472. doi: 10.1371/journal.pone.0023472. Epub 2011 Aug 22.
3. Escobar ML, etal., Apoptosis. 2008 Oct;13(10):1253-66.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Himeno M, etal., FEBS Lett 1989 Feb 27;244(2):351-6.
7. Howe CL, etal., Proc Natl Acad Sci U S A 1988 Oct;85(20):7577-81.
8. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
9. Lee HW, etal., J Neurosci. 2010 Apr 21;30(16):5508-18. doi: 10.1523/JNEUROSCI.4283-09.2010.
10. Mehrpour M, etal., Cell Res. 2010 Jul;20(7):748-62. Epub 2010 Jun 15.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Pipeline to import KEGG annotations from KEGG into RGD
14. RGD automated data pipeline
15. RGD automated import pipeline for gene-chemical interactions
16. RGD comprehensive gene curation
17. Shichiri M, etal., J Biol Chem. 2012 Jan 20;287(4):2926-34. doi: 10.1074/jbc.M111.321281. Epub 2011 Dec 6.
18. Storch S, etal., J Biol Chem. 2004 Dec 17;279(51):53625-34. doi: 10.1074/jbc.M410930200. Epub 2004 Oct 5.
19. Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Wasano K and Hirakawa Y, Histochemistry. 1994 Nov;102(5):329-35.
22. Wohlgemuth SE, etal., Rejuvenation Res. 2007 Sep;10(3):281-92.
Additional References at PubMed
PMID:10787428   PMID:11182090   PMID:11266470   PMID:11486041   PMID:11854359   PMID:12446704   PMID:12925704   PMID:14506282   PMID:14627652   PMID:14643301   PMID:14668490   PMID:15006695  
PMID:15052268   PMID:15073168   PMID:15292400   PMID:15294975   PMID:15588329   PMID:15613468   PMID:15792797   PMID:16415873   PMID:16542649   PMID:16674683   PMID:16973387   PMID:17620357  
PMID:18388320   PMID:18477453   PMID:18767904   PMID:18787122   PMID:19056867   PMID:19915045   PMID:19946888   PMID:20956541   PMID:21266579   PMID:22190682   PMID:22641697   PMID:22792322  
PMID:23376485   PMID:23395172   PMID:23533145   PMID:23632890   PMID:23704327   PMID:23926254   PMID:24029230   PMID:24035762   PMID:24841562   PMID:26284655   PMID:26329516   PMID:26432893  
PMID:26965651   PMID:27466344   PMID:29273596   PMID:30922709   PMID:31006538   PMID:33450132  


Genomics

Comparative Map Data
Lamp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21676,355,982 - 76,380,700 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1676,355,984 - 76,381,883 (-)Ensembl
Rnor_6.01681,689,576 - 81,714,341 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,689,335 - 81,714,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,175,574 - 81,200,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,213,165 - 81,230,019 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11681,213,425 - 81,230,284 (-)NCBI
Celera1674,162,536 - 74,179,021 (-)NCBICelera
RH 3.4 Map16744.4RGD
Cytogenetic Map16q12.5NCBI
LAMP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13113,297,239 - 113,323,672 (+)EnsemblGRCh38hg38GRCh38
GRCh3813113,297,239 - 113,323,672 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713113,951,554 - 113,977,987 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613112,999,470 - 113,025,742 (+)NCBINCBI36hg18NCBI36
Build 3413112,999,602 - 113,025,741NCBI
Celera1394,778,100 - 94,804,252 (+)NCBI
Cytogenetic Map13q34NCBI
HuRef1394,390,382 - 94,416,378 (+)NCBIHuRef
CHM1_113113,920,516 - 113,946,732 (+)NCBICHM1_1
Lamp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39813,209,161 - 13,225,338 (+)NCBIGRCm39mm39
GRCm39 Ensembl813,209,161 - 13,225,338 (+)Ensembl
GRCm38813,159,161 - 13,175,338 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,159,161 - 13,175,338 (+)EnsemblGRCm38mm10GRCm38
MGSCv37813,159,135 - 13,175,338 (+)NCBIGRCm37mm9NCBIm37
MGSCv36813,159,256 - 13,175,315 (+)NCBImm8
Celera813,327,454 - 13,343,657 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.73NCBI
Lamp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955404557,862 - 573,379 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955404557,090 - 573,532 (-)NCBIChiLan1.0ChiLan1.0
LAMP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113113,507,400 - 113,530,179 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13113,507,401 - 113,530,457 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01394,442,507 - 94,464,061 (+)NCBIMhudiblu_PPA_v0panPan3
LAMP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12260,678,116 - 60,695,619 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2260,678,111 - 60,694,924 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2260,390,142 - 60,407,645 (+)NCBI
ROS_Cfam_1.02261,363,372 - 61,380,853 (+)NCBI
UMICH_Zoey_3.12260,802,204 - 60,819,682 (+)NCBI
UNSW_CanFamBas_1.02260,804,391 - 60,821,868 (+)NCBI
UU_Cfam_GSD_1.02260,835,472 - 60,852,955 (+)NCBI
Lamp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945195,563,024 - 195,574,796 (+)NCBI
SpeTri2.0NW_004936472377,359 - 389,121 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LAMP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1178,600,713 - 78,617,615 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11178,600,818 - 78,617,587 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,117,963 - 86,134,737 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LAMP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1391,295,758 - 91,319,881 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl391,295,681 - 91,321,333 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604648,343,222 - 48,368,545 (+)NCBIVero_WHO_p1.0
Lamp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624793661,322 - 675,603 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
J03881  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,356,031 - 76,356,139 (+)MAPPERmRatBN7.2
Rnor_6.01681,689,385 - 81,689,492NCBIRnor6.0
Rnor_5.01681,175,624 - 81,175,731UniSTSRnor5.0
RGSC_v3.41681,212,972 - 81,213,079UniSTSRGSC3.4
Celera1674,162,346 - 74,162,453UniSTS
Cytogenetic Map16q12.5UniSTS
Lamp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,356,028 - 76,356,561 (+)MAPPERmRatBN7.2
Rnor_6.01681,689,382 - 81,689,913NCBIRnor6.0
Rnor_5.01681,175,621 - 81,176,152UniSTSRnor5.0
RGSC_v3.41681,212,969 - 81,213,499UniSTSRGSC3.4
Celera1674,162,343 - 74,162,873UniSTS
Cytogenetic Map16q12.5UniSTS
RH142299  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,363,174 - 76,363,728 (+)MAPPERmRatBN7.2
Rnor_6.01681,696,818 - 81,697,371NCBIRnor6.0
Rnor_5.01681,183,057 - 81,183,610UniSTSRnor5.0
Celera1674,169,278 - 74,169,831UniSTS
RH 3.4 Map16744.4UniSTS
Cytogenetic Map16q12.5UniSTS
RH137106  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,357,622 - 76,357,812 (+)MAPPERmRatBN7.2
Rnor_6.01681,690,975 - 81,691,164NCBIRnor6.0
Rnor_5.01681,177,214 - 81,177,403UniSTSRnor5.0
RGSC_v3.41681,214,561 - 81,214,750UniSTSRGSC3.4
Celera1674,163,935 - 74,164,124UniSTS
RH 3.4 Map16743.2UniSTS
Cytogenetic Map16q12.5UniSTS
BI282190  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,356,332 - 76,356,516 (+)MAPPERmRatBN7.2
Rnor_6.01681,689,685 - 81,689,868NCBIRnor6.0
Rnor_5.01681,175,924 - 81,176,107UniSTSRnor5.0
RGSC_v3.41681,213,271 - 81,213,454UniSTSRGSC3.4
Celera1674,162,645 - 74,162,828UniSTS
RH 3.4 Map16744.3UniSTS
Cytogenetic Map16q12.5UniSTS
UniSTS:143756  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,355,996 - 76,356,148 (+)MAPPERmRatBN7.2
Rnor_6.01681,689,350 - 81,689,501NCBIRnor6.0
Rnor_5.01681,175,589 - 81,175,740UniSTSRnor5.0
RGSC_v3.41681,212,937 - 81,213,088UniSTSRGSC3.4
Celera1674,162,311 - 74,162,462UniSTS
Cytogenetic Map16q12.5UniSTS
UniSTS:224778  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,356,689 - 76,356,843 (+)MAPPERmRatBN7.2
Rnor_6.01681,690,042 - 81,690,195NCBIRnor6.0
Rnor_5.01681,176,281 - 81,176,434UniSTSRnor5.0
RGSC_v3.41681,213,628 - 81,213,781UniSTSRGSC3.4
Celera1674,163,002 - 74,163,155UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:434
Count of miRNA genes:245
Interacting mature miRNAs:287
Transcripts:ENSRNOT00000026580
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026580   ⟹   ENSRNOP00000026580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,355,984 - 76,381,467 (-)Ensembl
Rnor_6.0 Ensembl1681,689,335 - 81,706,664 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,697,315 - 81,697,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092353   ⟹   ENSRNOP00000075799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,690,613 - 81,693,000 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092552   ⟹   ENSRNOP00000075832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,355,984 - 76,381,883 (-)Ensembl
Rnor_6.0 Ensembl1681,706,431 - 81,714,346 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092722
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,713,614 - 81,714,419 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096958   ⟹   ENSRNOP00000084480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,355,984 - 76,372,770 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105987   ⟹   ENSRNOP00000096531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,355,984 - 76,366,679 (-)Ensembl
RefSeq Acc Id: NM_012857   ⟹   NP_036989
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,356,224 - 76,372,920 (-)NCBI
Rnor_6.01681,689,576 - 81,706,561 (-)NCBI
Rnor_5.01681,175,574 - 81,200,580 (-)NCBI
RGSC_v3.41681,213,165 - 81,230,019 (-)RGD
Celera1674,162,536 - 74,179,021 (-)RGD
Sequence:
RefSeq Acc Id: XM_017599994   ⟹   XP_017455483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,355,982 - 76,380,700 (-)NCBI
Rnor_6.01681,689,963 - 81,714,341 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036989   ⟸   NM_012857
- Peptide Label: precursor
- UniProtKB: P14562 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455483   ⟸   XM_017599994
- Peptide Label: isoform X1
- UniProtKB: P14562 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075799   ⟸   ENSRNOT00000092353
RefSeq Acc Id: ENSRNOP00000075832   ⟸   ENSRNOT00000092552
RefSeq Acc Id: ENSRNOP00000026580   ⟸   ENSRNOT00000026580
RefSeq Acc Id: ENSRNOP00000084480   ⟸   ENSRNOT00000096958
RefSeq Acc Id: ENSRNOP00000096531   ⟸   ENSRNOT00000105987

Transcriptome

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

Promoters
RGD ID:13700232
Promoter ID:EPDNEW_R10756
Type:initiation region
Name:Lamp1_1
Description:lysosomal-associated membrane protein 1
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_6.01681,706,570 - 81,706,630EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/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)
FHH/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
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 81180941 81180942 C T snv BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2989 AgrOrtholog
Ensembl Genes ENSRNOG00000019629 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026580 UniProtKB/Swiss-Prot
  ENSRNOP00000075799 UniProtKB/TrEMBL
  ENSRNOP00000075832 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026580 UniProtKB/Swiss-Prot
  ENSRNOT00000092353 UniProtKB/TrEMBL
  ENSRNOT00000092552 UniProtKB/TrEMBL
InterPro LAMP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lysosome-assoc_membr_glycop UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25328 UniProtKB/Swiss-Prot
NCBI Gene 25328 ENTREZGENE
PANTHER PTHR11506 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lamp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lamp1 PhenoGen
PRINTS LYSASSOCTDMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE LAMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC203955
UniProt A0A0U1RRS9_RAT UniProtKB/TrEMBL
  A0A0U1RRW1_RAT UniProtKB/TrEMBL
  A0A6F8P9J1_RAT UniProtKB/TrEMBL
  LAMP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P97620 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-15 Lamp1  lysosomal-associated membrane protein 1  Lamp1  lysosomal membrane glycoprotein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Lamp1  Lysosomal associated membrane protein 1 (120 kDa)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains 20 potential N-glycosylation sites 729151
gene_expression expressed in liver, kidney, brain, lung, spleen, heart and pancreas 729151