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

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Gene: Map1lc3b2 (microtubule-associated protein 1 light chain 3 beta 2) Rattus norvegicus
Analyze
Symbol: Map1lc3b2 (Ensembl: AABR07026424.1)
Name: microtubule-associated protein 1 light chain 3 beta 2
RGD ID: 2323116
Description: Predicted to be located in intracellular membrane-bounded organelle; INTERACTS WITH aristolochic acid A (ortholog); arsenous acid (ortholog); astaxanthin (ortholog).
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
Human
Bonobo
Alliance Genes
More Info more info ...
Related Functional Gene: Map1lc3b  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,993,893 - 70,994,586 (-)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


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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

Comparative Map Data
Map1lc3b2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,993,893 - 70,994,586 (-)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
MAP1LC3B2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812116,559,381 - 116,576,606 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12116,548,105 - 116,576,606 (+)EnsemblGRCh38hg38GRCh38
GRCh3712116,997,186 - 117,014,411 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612115,481,569 - 115,498,808 (+)NCBINCBI36Build 36hg18NCBI36
Celera12116,626,684 - 116,643,942 (+)NCBICelera
Cytogenetic Map12q24.22NCBI
HuRef12114,006,308 - 114,023,538 (+)NCBIHuRef
CHM1_112116,964,836 - 116,982,072 (+)NCBICHM1_1
T2T-CHM13v2.012116,540,616 - 116,557,802 (+)NCBIT2T-CHM13v2.0
MAP1LC3B2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan112124,614,185 - 124,632,826 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012114,134,551 - 114,151,817 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112117,527,702 - 117,528,447 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12117,527,789 - 117,528,166 (+)Ensemblpanpan1.1panPan2

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
RefSeq Status:
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21670,993,893 - 70,994,586 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038950872 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000075089   ⟸   ENSRNOT00000019033
RefSeq Acc Id: XP_038950872   ⟸   XM_039094944

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, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075089.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019033.6 UniProtKB/TrEMBL
InterPro Atg8-like UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/TrEMBL
NCBI Gene 100359928 ENTREZGENE
PANTHER MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3 BETA 2-RELATED UniProtKB/TrEMBL
  PTHR10969 UniProtKB/TrEMBL
Pfam Atg8 UniProtKB/TrEMBL
PhenoGen Map1lc3b2 PhenoGen
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt A0A0G2K9Q7_RAT UniProtKB/TrEMBL


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