Human Gene MAP1LC3A (ENST00000360668.8_4) from GENCODE V47lift37
  Description: microtubule associated protein 1 light chain 3 alpha, transcript variant 1 (from RefSeq NM_032514.4)
Gencode Transcript: ENST00000360668.8_4
Gencode Gene: ENSG00000101460.13_7
Transcript (Including UTRs)
   Position: hg19 chr20:33,146,522-33,148,149 Size: 1,628 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr20:33,146,673-33,147,702 Size: 1,030 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:33,146,522-33,148,149)mRNA (may differ from genome)Protein (121 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MLP3A_HUMAN
DESCRIPTION: RecName: Full=Microtubule-associated proteins 1A/1B light chain 3A; AltName: Full=Autophagy-related protein LC3 A; AltName: Full=Autophagy-related ubiquitin-like modifier LC3 A; AltName: Full=MAP1 light chain 3-like protein 1; AltName: Full=MAP1A/MAP1B light chain 3 A; Short=MAP1A/MAP1B LC3 A; AltName: Full=Microtubule-associated protein 1 light chain 3 alpha; Flags: Precursor;
FUNCTION: Probably involved in formation of autophagosomal vacuoles (autophagosomes).
SUBUNIT: 3 different light chains, LC1, LC2 and LC3, can associate with MAP1A and MAP1B proteins (By similarity). Interacts with SQSTM1 (By similarity). Interacts with TP53INP1 and TP53INP2.
INTERACTION: Q14596:NBR1; NbExp=2; IntAct=EBI-720768, EBI-742698; Q13501:SQSTM1; NbExp=5; IntAct=EBI-720768, EBI-307104;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Endomembrane system; Lipid-anchor. Cytoplasmic vesicle, autophagosome membrane; Lipid-anchor. Cytoplasmic vesicle, autophagosome. Note=LC3-II binds to the autophagic membranes.
TISSUE SPECIFICITY: Most abundant in heart, brain, liver, skeletal muscle and testis but absent in thymus and peripheral blood leukocytes.
PTM: The precursor molecule is cleaved by APG4B/ATG4B to form the cytosolic form, LC3-I. This is activated by APG7L/ATG7, transferred to ATG3 and conjugated to phospholipid to form the membrane-bound form, LC3-II.
SIMILARITY: Belongs to the MAP1 LC3 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: MAP1LC3A
Diseases sorted by gene-association score: nasu-hakola disease (3), leber congenital amaurosis 6 (3), lacrimal gland adenocarcinoma (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 75.82 RPKM in Brain - Cerebellum
Total median expression: 1557.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.90151-0.390 Picture PostScript Text
3' UTR -196.20447-0.439 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004241 - Atg8_ubiquitin-like

Pfam Domains:
PF02991 - Autophagy protein Atg8 ubiquitin like
PF04110 - Ubiquitin-like autophagy protein Apg12

SCOP Domains:
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3ECI - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9H492
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0008429 phosphatidylethanolamine binding
GO:0031625 ubiquitin protein ligase binding

Biological Process:
GO:0000045 autophagosome assembly
GO:0000422 mitophagy
GO:0006914 autophagy
GO:0006995 cellular response to nitrogen starvation
GO:0009267 cellular response to starvation
GO:0010040 response to iron(II) ion
GO:0010288 response to lead ion
GO:0016236 macroautophagy
GO:0031667 response to nutrient levels
GO:0034198 cellular response to amino acid starvation
GO:0043278 response to morphine
GO:0070301 cellular response to hydrogen peroxide
GO:0071280 cellular response to copper ion
GO:0097352 autophagosome maturation

Cellular Component:
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005770 late endosome
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0031090 organelle membrane
GO:0031410 cytoplasmic vesicle
GO:0044754 autolysosome


-  Descriptions from all associated GenBank mRNAs
  LP896221 - Sequence 1085 from Patent EP3253886.
AF276658 - Homo sapiens MAP1 light chain 3-like protein 1 mRNA, complete cds.
JD416346 - Sequence 397370 from Patent EP1572962.
BC015810 - Homo sapiens microtubule-associated protein 1 light chain 3 alpha, mRNA (cDNA clone MGC:9521 IMAGE:3909192), complete cds.
AL833855 - Homo sapiens mRNA; cDNA DKFZp761L0515 (from clone DKFZp761L0515).
JD306616 - Sequence 287640 from Patent EP1572962.
AB528175 - Synthetic construct DNA, clone: pF1KE0125, Homo sapiens MAP1LC3A gene for microtubule-associated protein 1 light chain 3 alpha, without stop codon, in Flexi system.
KJ895007 - Synthetic construct Homo sapiens clone ccsbBroadEn_04401 MAP1LC3A gene, encodes complete protein.
BT007452 - Homo sapiens microtubule-associated protein 1 light chain 3 alpha mRNA, complete cds.
DQ893641 - Synthetic construct clone IMAGE:100006271; FLH185386.01X; RZPDo839A08148D microtubule-associated protein 1 light chain 3 alpha (MAP1LC3A) gene, encodes complete protein.
DQ895536 - Synthetic construct Homo sapiens clone IMAGE:100009996; FLH185382.01L; RZPDo839A08147D microtubule-associated protein 1 light chain 3 alpha (MAP1LC3A) gene, encodes complete protein.
AM392590 - Synthetic construct Homo sapiens clone IMAGE:100002032 for hypothetical protein (MAP1LC3A gene).
JD545007 - Sequence 526031 from Patent EP1572962.
JD466240 - Sequence 447264 from Patent EP1572962.
JD498379 - Sequence 479403 from Patent EP1572962.
JD356174 - Sequence 337198 from Patent EP1572962.
JD498639 - Sequence 479663 from Patent EP1572962.
JD371478 - Sequence 352502 from Patent EP1572962.
JD121744 - Sequence 102768 from Patent EP1572962.
JD133600 - Sequence 114624 from Patent EP1572962.
JD086705 - Sequence 67729 from Patent EP1572962.
JD527990 - Sequence 509014 from Patent EP1572962.
JD535041 - Sequence 516065 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H492 (Reactome details) participates in the following event(s):

R-HSA-5205649 p62 links damaged mitochondria to LC3
R-HSA-8959573 Phosphorylated FUNDC1 links damaged mitochondria to LC3
R-HSA-5681987 LC3 is cleaved by ATG4
R-HSA-5682377 LC3 de-lipidation by ATG4
R-HSA-5205663 LC3 binds the autophagosome membrane Atg5-Atg12 complex
R-HSA-8959571 LC3 binds the autophagosome membrane Atg5-Atg12 complex
R-HSA-5678490 ATG16L1 complex transfers LC3 from ATG3 to PE
R-HSA-5683593 ATG7:ATG3:LC3 dissociates
R-HSA-5682896 LC3:ATG7 dimer binds ATG3
R-HSA-5681981 ATG3 transfers LC3 from ATG7 to ATG3
R-HSA-5205685 Pink/Parkin Mediated Mitophagy
R-HSA-8934903 Receptor Mediated Mitophagy
R-HSA-1632852 Macroautophagy
R-HSA-5205647 Mitophagy
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: E1P5P4, E1P5P5, ENST00000360668.1, ENST00000360668.2, ENST00000360668.3, ENST00000360668.4, ENST00000360668.5, ENST00000360668.6, ENST00000360668.7, MLP3A_HUMAN, NM_032514, Q9BXW5, Q9H492, uc318brg.1, uc318brg.2
UCSC ID: ENST00000360668.8_4
RefSeq Accession: NM_032514.4
Protein: Q9H492 (aka MLP3A_HUMAN or MP3A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.