Map1lc3b (microtubule-associated protein 1 light chain 3 beta) - Rat Genome Database

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Gene: Map1lc3b (microtubule-associated protein 1 light chain 3 beta) Rattus norvegicus
Analyze
Symbol: Map1lc3b
Name: microtubule-associated protein 1 light chain 3 beta
RGD ID: 621315
Description: Exhibits microtubule binding activity and protein domain specific binding activity. Involved in positive regulation of protein binding activity. Localizes to several cellular components, including autophagosome membrane; microtubule associated complex; and neuronal cell body. Orthologous to several human genes including MAP1LC3B (microtubule associated protein 1 light chain 3 beta); PARTICIPATES IN autophagy pathway; INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrobenzenesulfonic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: autophagy-related protein LC3 B; autophagy-related ubiquitin-like modifier LC3 B; LC3B; MAP1 light chain 3-like protein 2; MAP1A/1B light chain 3 B; MAP1A/MAP1B LC3 B; MAP1A/MAP1B light chain 3 B; Map1lc3; MGC93422; microtubule-associated proteins 1A/1B light chain 3; microtubule-associated proteins 1A/1B light chain 3B; MPL3; zbs559
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
mRatBN7.21949,665,795 - 49,673,655 (+)NCBI
Rnor_6.0 Ensembl1953,629,779 - 53,646,058 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01953,635,449 - 53,643,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01964,373,068 - 64,381,400 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,847,187 - 51,854,858 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11951,852,067 - 51,859,738 (+)NCBI
Celera1948,912,797 - 48,920,467 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-Tetrandrine  (ISO)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-deoxy-D-glucose  (ISO)
2-hydroxyethyl methacrylate  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
3-methyladenine  (EXP,ISO)
3-Nitrofluoranthene  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (EXP,ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
7-ketocholesterol  (ISO)
acadesine  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acrylamide  (EXP,ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
aloxistatin  (ISO)
alpha,alpha-trehalose  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP,ISO)
amphotericin B  (ISO)
apigenin  (ISO)
apocynin  (EXP)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (EXP,ISO)
artesunate  (ISO)
atazanavir sulfate  (ISO)
auramine O  (ISO)
AZD4547  (ISO)
bafilomycin A1  (EXP,ISO)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-lapachone  (ISO)
betulinic acid  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
bortezomib  (ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calix[6]arene  (ISO)
Calpeptin  (ISO)
carbon disulfide  (ISO)
carbon nanotube  (ISO)
carglumic acid  (ISO)
celecoxib  (ISO)
CGS-21680  (ISO)
chenodeoxycholic acid  (ISO)
chloropicrin  (ISO)
chloroquine  (EXP,ISO)
chlorpyrifos  (EXP)
cholesterol  (ISO)
cholic acid  (ISO)
chromium(6+)  (ISO)
chrysin  (EXP)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP,ISO)
Citreoviridin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
cobalt dichloride  (ISO)
colistin  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cryptotanshinone  (ISO)
cyanamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP)
DDE  (ISO)
Dehydroeburicoic acid  (ISO)
deoxycholic acid  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenzofuran  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
diquat  (ISO)
disodium selenite  (EXP,ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
ferric oxide  (ISO)
finasteride  (EXP)
flavokawain B  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fomepizole  (ISO)
formaldehyde  (EXP,ISO)
gamma-hexachlorocyclohexane  (EXP)
gingerol  (ISO)
ginsenoside Rg2  (ISO)
glafenine  (EXP)
glucose  (EXP)
glutathione  (EXP,ISO)
glycerol 2-phosphate  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhizinic acid  (EXP)
hexadecanoic acid  (EXP,ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (ISO)
indoxyl sulfate  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
juglone  (ISO)
kainic acid  (EXP)
L-ascorbic acid 2-phosphate  (ISO)
L-leucine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (EXP,ISO)
luteolin  (ISO)
LY294002  (EXP)
mannose  (ISO)
menadione  (ISO)
metformin  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
metyrapone  (ISO)
myriocin  (ISO)
N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
Naftopidil  (ISO)
nefazodone  (EXP,ISO)
nelfinavir  (ISO)
niclosamide  (ISO)
nicotinamide  (ISO)
nimesulide  (EXP)
Nonylphenol  (EXP)
obeticholic acid  (ISO)
oleanolic acid  (ISO)
oleic acid  (ISO)
oxidopamine  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PD 0325901  (ISO)
pepstatin A  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphatidylethanolamine  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
procyanidin B2  (ISO)
quercetin  (ISO)
quetiapine fumarate  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rimonabant  (ISO)
rotenone  (EXP,ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sirolimus  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (EXP,ISO)
Soman  (EXP)
spironolactone  (EXP)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
T-2 toxin  (EXP)
tamoxifen  (ISO)
taurine  (ISO)
taurocholic acid  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thalidomide  (ISO)
thapsigargin  (EXP,ISO)
thiamine(1+) chloride  (EXP,ISO)
titanium dioxide  (ISO)
trametinib  (ISO)
trichostatin A  (EXP,ISO)
trifloxystrobin  (ISO)
trimethyltin  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vincristine  (ISO)
vorinostat  (EXP,ISO)
wortmannin  (ISO)
zearalenone  (EXP)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11060023   PMID:14760703   PMID:15095872   PMID:15489334   PMID:16854843   PMID:19279012   PMID:22783020   PMID:22948227   PMID:23629966   PMID:24089209   PMID:24185898   PMID:24351649  
PMID:24747438   PMID:25127057   PMID:25215947   PMID:25244949   PMID:25494214   PMID:26284655   PMID:27187184   PMID:27442348   PMID:28223137   PMID:29554128   PMID:29901175   PMID:31140414  


Genomics

Comparative Map Data
Map1lc3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21949,665,795 - 49,673,655 (+)NCBI
Rnor_6.0 Ensembl1953,629,779 - 53,646,058 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01953,635,449 - 53,643,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01964,373,068 - 64,381,400 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,847,187 - 51,854,858 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11951,852,067 - 51,859,738 (+)NCBI
Celera1948,912,797 - 48,920,467 (+)NCBICelera
Cytogenetic Map19q12NCBI
MAP1LC3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1687,383,953 - 87,404,779 (+)EnsemblGRCh38hg38GRCh38
GRCh381687,392,336 - 87,404,774 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371687,425,942 - 87,438,380 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361685,983,320 - 85,995,881 (+)NCBINCBI36hg18NCBI36
Build 341685,983,450 - 85,995,880NCBI
Celera1671,722,569 - 71,735,146 (+)NCBI
Cytogenetic Map16q24.2NCBI
HuRef1673,168,889 - 73,180,793 (+)NCBIHuRef
CHM1_11688,837,611 - 88,850,167 (+)NCBICHM1_1
Map1lc3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398122,317,177 - 122,325,499 (+)NCBIGRCm39mm39
GRCm39 Ensembl8122,317,100 - 122,325,499 (+)Ensembl
GRCm388121,590,438 - 121,598,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,590,361 - 121,598,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv378124,114,368 - 124,121,947 (+)NCBIGRCm37mm9NCBIm37
MGSCv368124,476,528 - 124,484,107 (+)NCBImm8
Celera8125,811,811 - 125,819,390 (+)NCBICelera
Cytogenetic Map8E1NCBI
Map1lc3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555411,852,388 - 1,868,194 (+)NCBIChiLan1.0ChiLan1.0
MAP1LC3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11687,393,976 - 87,399,736 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01668,063,869 - 68,076,772 (+)NCBIMhudiblu_PPA_v0panPan3
MAP1LC3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1565,669,553 - 65,683,445 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha565,681,248 - 65,695,108 (-)NCBI
ROS_Cfam_1.0565,891,103 - 65,905,466 (-)NCBI
UMICH_Zoey_3.1565,915,961 - 65,929,771 (-)NCBI
UNSW_CanFamBas_1.0565,747,849 - 65,761,805 (-)NCBI
UU_Cfam_GSD_1.0566,161,995 - 66,175,961 (-)NCBI
MAP1LC3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl61,915,387 - 1,941,077 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.161,919,879 - 1,941,069 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.262,007,809 - 2,029,003 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MAP1LC3B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1572,762,428 - 72,774,204 (+)NCBI
Map1lc3b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247463,084,418 - 3,094,250 (+)NCBI

Position Markers
RH128740  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01953,643,815 - 53,643,967NCBIRnor6.0
Rnor_5.01964,381,250 - 64,381,402UniSTSRnor5.0
RGSC_v3.41951,854,708 - 51,854,860UniSTSRGSC3.4
Celera1948,920,317 - 48,920,469UniSTS
RH 3.4 Map19680.7UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:288
Count of miRNA genes:193
Interacting mature miRNAs:226
Transcripts:ENSRNOT00000051352, ENSRNOT00000067141
Prediction methods:Microtar, Miranda, 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: ENSRNOT00000051352   ⟹   ENSRNOP00000049421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1953,629,779 - 53,646,055 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067141   ⟹   ENSRNOP00000062130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1953,635,688 - 53,643,964 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079382   ⟹   ENSRNOP00000072338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1953,635,445 - 53,646,058 (+)Ensembl
RefSeq Acc Id: NM_022867   ⟹   NP_074058
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21949,665,979 - 49,673,650 (+)NCBI
Rnor_6.01953,635,633 - 53,643,965 (+)NCBI
Rnor_5.01964,373,068 - 64,381,400 (+)NCBI
RGSC_v3.41951,847,187 - 51,854,858 (+)RGD
Celera1948,912,797 - 48,920,467 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601351   ⟹   XP_017456840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21949,665,795 - 49,673,655 (+)NCBI
Rnor_6.01953,635,449 - 53,643,970 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_074058   ⟸   NM_022867
- UniProtKB: Q62625 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017456840   ⟸   XM_017601351
- Peptide Label: isoform X1
- UniProtKB: Q62625 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072338   ⟸   ENSRNOT00000079382
RefSeq Acc Id: ENSRNOP00000062130   ⟸   ENSRNOT00000067141
RefSeq Acc Id: ENSRNOP00000049421   ⟸   ENSRNOT00000051352

Transcriptome

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

Promoters
RGD ID:13701192
Promoter ID:EPDNEW_R11715
Type:initiation region
Name:Map1lc3b_1
Description:microtubule-associated protein 1 light chain 3 beta
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_6.01953,635,650 - 53,635,710EPDNEW

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)
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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)
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
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621315 AgrOrtholog
Ensembl Genes ENSRNOG00000017905 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000049421 UniProtKB/TrEMBL
  ENSRNOP00000062130 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000072338 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051352 UniProtKB/TrEMBL
  ENSRNOT00000067141 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000079382 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6889616 IMAGE-MGC_LOAD
  IMAGE:7189855 IMAGE-MGC_LOAD
InterPro Atg8-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64862 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72811 IMAGE-MGC_LOAD
  MGC:93422 IMAGE-MGC_LOAD
NCBI Gene 64862 ENTREZGENE
PANTHER PTHR10969 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Atg8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Map1lc3b PhenoGen
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt MLP3B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q7TQ75_RAT UniProtKB/TrEMBL
UniProt Secondary Q6XVN7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Map1lc3b  microtubule-associated protein 1 light chain 3 beta    microtubule-associated proteins 1A/1B light chain 3  Name updated 1299863 APPROVED
2004-09-10 Map1lc3b  microtubule-associated proteins 1A/1B light chain 3  MPL3    Symbol and Name updated 1299863 APPROVED
2002-08-07 MPL3  microtubule-associated proteins 1A/1B light chain 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed only in neurons 633201
gene_protein 16.4 kDa 633201