Map1lc3b2 (microtubule-associated protein 1 light chain 3 beta 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Map1lc3b2 (microtubule-associated protein 1 light chain 3 beta 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Map1lc3b2
Name: microtubule-associated protein 1 light chain 3 beta 2
RGD ID: 2323116
Description:
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: LOC100359928; microtubule-associated protein 1 light chain 3 beta-like; microtubule-associated proteins 1A/1B light chain 3B-like
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Map1lc3b  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,696,531 - 77,696,983 (-)NCBIGRCr8
mRatBN7.21670,994,128 - 70,994,580 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,994,128 - 70,994,606 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01675,864,144 - 75,874,567 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,873,881 - 75,874,519 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,478,598 - 75,479,179 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,796,820 - 75,797,899 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,839,898 - 68,840,608 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Map1lc3b2
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:69
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000019033
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
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
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat

Markers in Region
RH144058  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,022,195 - 71,022,423 (+)MAPPERmRatBN7.2
Rnor_6.01675,900,934 - 75,901,161NCBIRnor6.0
Rnor_5.01675,506,639 - 75,506,866UniSTSRnor5.0
RGSC_v3.41675,824,839 - 75,825,066UniSTSRGSC3.4
Celera1668,868,219 - 68,868,446UniSTS
RH 3.4 Map16693.6UniSTS
BE119431  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21671,024,524 - 71,024,686 (+)MAPPERmRatBN7.2
Rnor_6.01675,903,263 - 75,903,424NCBIRnor6.0
Rnor_5.01675,508,968 - 75,509,129UniSTSRnor5.0
RGSC_v3.41675,827,168 - 75,827,329UniSTSRGSC3.4
Celera1668,870,548 - 68,870,709UniSTS
RH 3.4 Map16702.7UniSTS


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: ENSRNOT00000019033   ⟹   ENSRNOP00000075089
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,994,128 - 70,994,606 (-)Ensembl
Rnor_6.0 Ensembl1675,873,881 - 75,874,519 (-)Ensembl
RefSeq Acc Id: XM_039094944   ⟹   XP_038950872
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21670,993,893 - 70,994,586 (-)NCBI
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K9Q7-F1-model_v2 AlphaFold A0A0G2K9Q7 1-125 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-10806 BioCyc
Ensembl Genes ENSRNOG00000038106 Ensembl, ENTREZGENE
NCBI Gene 100359928 ENTREZGENE
PhenoGen Map1lc3b2 PhenoGen
RatGTEx ENSRNOG00000038106 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Map1lc3b2  microtubule-associated protein 1 light chain 3 beta 2  LOC100359928  microtubule-associated protein 1 light chain 3 beta-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100359928  microtubule-associated protein 1 light chain 3 beta-like      Symbol and Name status set to provisional 70820 PROVISIONAL