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Aliases for MAP1LC3A Gene

Aliases for MAP1LC3A Gene

  • Microtubule Associated Protein 1 Light Chain 3 Alpha 2 3 5
  • Autophagy-Related Ubiquitin-Like Modifier LC3 A 3 4
  • MAP1 Light Chain 3-Like Protein 1 3 4
  • MAP1A/MAP1B Light Chain 3 A 3 4
  • MAP1A/MAP1B LC3 A 3 4
  • Microtubule-Associated Proteins 1A/1B Light Chain 3A 3
  • Microtubule-Associated Protein 1 Light Chain 3 Alpha 4
  • Microtubule-Associated Proteins 1A/1B Light Chain 3 3
  • Autophagy-Related Protein LC3 A 4
  • MAP1A/1B Light Chain 3 A 3
  • MAP1ALC3 3
  • MAP1BLC3 3
  • ATG8E 3
  • LC3A 3
  • LC3 3

External Ids for MAP1LC3A Gene

Previous GeneCards Identifiers for MAP1LC3A Gene

  • GC20P032896
  • GC20P033806
  • GC20P033850
  • GC20P032598
  • GC20P033134
  • GC20P029915

Summaries for MAP1LC3A Gene

Entrez Gene Summary for MAP1LC3A Gene

  • MAP1A and MAP1B are microtubule-associated proteins which mediate the physical interactions between microtubules and components of the cytoskeleton. MAP1A and MAP1B each consist of a heavy chain subunit and multiple light chain subunits. The protein encoded by this gene is one of the light chain subunits and can associate with either MAP1A or MAP1B. Two transcript variants encoding different isoforms have been found for this gene. The expression of variant 1 is suppressed in many tumor cell lines, suggesting that may be involved in carcinogenesis. [provided by RefSeq, Feb 2012]

GeneCards Summary for MAP1LC3A Gene

MAP1LC3A (Microtubule Associated Protein 1 Light Chain 3 Alpha) is a Protein Coding gene. Diseases associated with MAP1LC3A include Leber Congenital Amaurosis 6 and Lacrimal Gland Adenocarcinoma. Among its related pathways are Pink/Parkin Mediated Mitophagy and Ferroptosis. Gene Ontology (GO) annotations related to this gene include microtubule binding and phosphatidylethanolamine binding. An important paralog of this gene is MAP1LC3B.

UniProtKB/Swiss-Prot for MAP1LC3A Gene

  • Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes) (PubMed:20713600, PubMed:24290141). Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (PubMed:20713600).

Gene Wiki entry for MAP1LC3A Gene

Additional gene information for MAP1LC3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MAP1LC3A Gene

Genomics for MAP1LC3A Gene

GeneHancer (GH) Regulatory Elements for MAP1LC3A Gene

Promoters and enhancers for MAP1LC3A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J034557 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 650.4 +12.6 12554 3.1 CTCF ATF1 SIN3A RAD21 POLR2A ATF7 CREM SMARCA5 ZNF687 RXRA MAP1LC3A PIGU NCOA6 EIF6 MMP24OS ITCH GC20M034549
GH20J034546 Promoter/Enhancer 1 EPDnew ENCODE dbSUPER 650.7 +0.2 195 0.7 POLR2A MAP1LC3A TP53INP2 ENSG00000231034 PIGU GC20M034549
GH20J034514 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 33.3 -30.8 -30785 3.1 PKNOX1 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 POLR2B DYNLRB1 MAP1LC3A NCOA6 ZNF341-AS1 PIGU TRPC4AP EIF6 TP53INP2 ACTL10 ITCH
GH20J034522 Enhancer 1.4 Ensembl ENCODE dbSUPER 33.5 -21.8 -21803 5.9 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SLC30A9 ZNF143 GC20M034527 GC20P034523 ENSG00000206582 MAP1LC3A ZNF341-AS1 ACTL10 ITCH TP53INP2 ENSG00000231034 PIGU
GH20J034361 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 22.7 -183.8 -183752 3.2 HDGF SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ITCH MAP1LC3A CDK5RAP1 ZNF341-AS1 CBFA2T2 NCOA6 ENSG00000234087
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MAP1LC3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MAP1LC3A gene promoter:
  • MRF-2
  • NF-Y
  • CBF(2)
  • ER-alpha
  • NF-1
  • NF-1/L
  • IRF-1
  • Pax-6
  • AML1a
  • MyoD

Genomic Locations for MAP1LC3A Gene

Genomic Locations for MAP1LC3A Gene
13,516 bases
Plus strand
13,492 bases
Plus strand

Genomic View for MAP1LC3A Gene

Genes around MAP1LC3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MAP1LC3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MAP1LC3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MAP1LC3A Gene

Proteins for MAP1LC3A Gene

  • Protein details for MAP1LC3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Microtubule-associated proteins 1A/1B light chain 3A
    Protein Accession:
    Secondary Accessions:
    • E1P5P4
    • E1P5P5
    • Q9BXW5

    Protein attributes for MAP1LC3A Gene

    121 amino acids
    Molecular mass:
    14272 Da
    Quaternary structure:
    • 3 different light chains, LC1, LC2 and LC3, can associate with MAP1A and MAP1B proteins (By similarity). Interacts with TP53INP1 and TP53INP2 (PubMed:19056683, PubMed:22470510). Directly interacts with SQSTM1; this interaction leads to MAP1LC3A recruitment to inclusion bodies containing polyubiquitinated protein aggregates and to inclusion body degradation by autophagy (PubMed:17580304). Interacts with ATG13 (PubMed:24290141, PubMed:23043107). Interacts with ULK1 (PubMed:23043107). Interacts with TBC1D5 (PubMed:22354992). Found in a complex with UBQLN1 and UBQLN2 (PubMed:20529957). Interacts with UBQLN4 (via STI1 1 and 2 domains). Interacts with UBQLN1 in the presence of UBQLN4 (PubMed:23459205). Interacts with TRIM5 (PubMed:25127057). Interacts with MEFV (PubMed:26347139). Interacts with RETREG1, RETREG2 and RETREG3 (PubMed:26040720).

    Three dimensional structures from OCA and Proteopedia for MAP1LC3A Gene

    Alternative splice isoforms for MAP1LC3A Gene


neXtProt entry for MAP1LC3A Gene

Post-translational modifications for MAP1LC3A Gene

  • The precursor molecule is cleaved by 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 (PubMed:15187094).
  • The Legionella effector RavZ is a deconjugating enzyme that produces an ATG8 product that would be resistant to reconjugation by the host machinery due to the cleavage of the reactive C-terminal glycine.
  • Phosphorylation at Ser-12 by PKA inhibits conjugation to phosphatidylethanolamine (PE). Interaction with MAPK15 reduces the inhibitory phosphorylation and increases autophagy activity.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for MAP1LC3A Gene

Antibody Products

No data available for DME Specific Peptides for MAP1LC3A Gene

Domains & Families for MAP1LC3A Gene

Gene Families for MAP1LC3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for MAP1LC3A Gene

Suggested Antigen Peptide Sequences for MAP1LC3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ATG8 family.
  • Belongs to the ATG8 family.
genes like me logo Genes that share domains with MAP1LC3A: view

Function for MAP1LC3A Gene

Molecular function for MAP1LC3A Gene

UniProtKB/Swiss-Prot Function:
Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes) (PubMed:20713600, PubMed:24290141). Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (PubMed:20713600).

Phenotypes From GWAS Catalog for MAP1LC3A Gene

Gene Ontology (GO) - Molecular Function for MAP1LC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11096062
GO:0005543 phospholipid binding IDA 15187094
GO:0008017 microtubule binding IBA --
GO:0008429 phosphatidylethanolamine binding IDA 16303767
GO:0031625 ubiquitin protein ligase binding IPI 25127057
genes like me logo Genes that share ontologies with MAP1LC3A: view
genes like me logo Genes that share phenotypes with MAP1LC3A: view

Animal Model Products

CRISPR Products

miRNA for MAP1LC3A Gene

miRTarBase miRNAs that target MAP1LC3A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MAP1LC3A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for MAP1LC3A Gene

Localization for MAP1LC3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for MAP1LC3A Gene

Cytoplasm, cytoskeleton. Endomembrane system; Lipid-anchor. Cytoplasmic vesicle, autophagosome membrane; Lipid-anchor. Cytoplasmic vesicle, autophagosome. Note=LC3-II binds to the autophagic membranes.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MAP1LC3A gene
Compartment Confidence
cytosol 5
lysosome 5
cytoskeleton 4
nucleus 3
mitochondrion 2
endosome 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for MAP1LC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000421 autophagosome membrane TAS --
GO:0005737 cytoplasm IEA --
GO:0005770 late endosome IEA --
GO:0005776 autophagosome IDA,IEA 12740394
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with MAP1LC3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for MAP1LC3A Gene

Pathways & Interactions for MAP1LC3A Gene

genes like me logo Genes that share pathways with MAP1LC3A: view

Pathways by source for MAP1LC3A Gene

1 KEGG pathway for MAP1LC3A Gene
1 R&D Systems pathway for MAP1LC3A Gene

SIGNOR curated interactions for MAP1LC3A Gene

Is activated by:

Gene Ontology (GO) - Biological Process for MAP1LC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly ISS --
GO:0000422 autophagy of mitochondrion IGI 22267086
GO:0006914 autophagy IEA --
GO:0006995 cellular response to nitrogen starvation IBA --
GO:0009267 cellular response to starvation IDA 28223137
genes like me logo Genes that share ontologies with MAP1LC3A: view

Drugs & Compounds for MAP1LC3A Gene

(14) Drugs for MAP1LC3A Gene - From:

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cabazitaxel Approved Pharma 0
Docetaxel Approved, Investigational Pharma Microtubulin disassembly inhibitor, Tubulin and VEGF inhibitor, Taxanes 2040
Griseofulvin Approved, Investigational, Vet_approved Pharma 6
2-Methoxyestradiol (2-MeOE2) Pharma Apoptotic, antiproliferative and antiangiogenic agent 0
CK-636 Pharma Arp2/3 complex inhibitor 0
genes like me logo Genes that share compounds with MAP1LC3A: view

Transcripts for MAP1LC3A Gene

mRNA/cDNA for MAP1LC3A Gene

Unigene Clusters for MAP1LC3A Gene

Microtubule-associated protein 1 light chain 3 alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MAP1LC3A

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MAP1LC3A Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7
SP1: - - -
SP2: -

Relevant External Links for MAP1LC3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MAP1LC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MAP1LC3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MAP1LC3A Gene

This gene is overexpressed in Brain (14.8), Fetal Brain (13.4), Retina (10.9), Frontal cortex (8.3), and Spinal cord (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MAP1LC3A Gene

Protein tissue co-expression partners for MAP1LC3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MAP1LC3A Gene:


SOURCE GeneReport for Unigene cluster for MAP1LC3A Gene:


mRNA Expression by UniProt/SwissProt for MAP1LC3A Gene:

Tissue specificity: Most abundant in heart, brain, liver, skeletal muscle and testis but absent in thymus and peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for MAP1LC3A Gene

  • Nervous system(4.6)
  • Muscle(2.1)
  • Liver(2)
genes like me logo Genes that share expression patterns with MAP1LC3A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for MAP1LC3A Gene

Orthologs for MAP1LC3A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for MAP1LC3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MAP1LC3A 34 33
  • 98.35 (n)
(Bos Taurus)
Mammalia MAP1LC3A 34 33
  • 95.59 (n)
(Canis familiaris)
Mammalia MAP1LC3A 34 33
  • 95.04 (n)
(Rattus norvegicus)
Mammalia Map1lc3a 33
  • 93.39 (n)
(Mus musculus)
Mammalia Map1lc3a 16 34 33
  • 93.11 (n)
(Monodelphis domestica)
Mammalia MAP1LC3A 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia MAP1LC3A 34
  • 82 (a)
(Gallus gallus)
Aves MAP1LC3A 34 33
  • 85.95 (n)
(Anolis carolinensis)
Reptilia MAP1LC3A 34
  • 86 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia map1lc3a 33
  • 79.44 (n)
Str.13107 33
African clawed frog
(Xenopus laevis)
Amphibia map1lc3a-prov 33
(Danio rerio)
Actinopterygii map1lc3a 34 33
  • 81.11 (n)
wufc38e10 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8909 33
(Caenorhabditis elegans)
Secernentea lgg-2 34 35 33
  • 55.85 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATG8 34
  • 34 (a)
Species where no ortholog for MAP1LC3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for MAP1LC3A Gene

Gene Tree for MAP1LC3A (if available)
Gene Tree for MAP1LC3A (if available)
Evolutionary constrained regions (ECRs) for MAP1LC3A: view image

Paralogs for MAP1LC3A Gene

Paralogs for MAP1LC3A Gene

(8) SIMAP similar genes for MAP1LC3A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with MAP1LC3A: view

Variants for MAP1LC3A Gene

Sequence variations from dbSNP and Humsavar for MAP1LC3A Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000140497 -- 34,553,805(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000356100 -- 34,556,878(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000785166 -- 34,545,016(+) C/T upstream_transcript_variant
rs1000795569 -- 34,549,566(+) C/G/T genic_upstream_transcript_variant, intron_variant
rs1000834405 -- 34,556,318(+) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for MAP1LC3A Gene

Variant ID Type Subtype PubMed ID
esv2666225 CNV deletion 23128226
nsv3359 CNV deletion 18451855

Variation tolerance for MAP1LC3A Gene

Residual Variation Intolerance Score: 48% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.03; 0.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MAP1LC3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MAP1LC3A Gene

Disorders for MAP1LC3A Gene

MalaCards: The human disease database

(2) MalaCards diseases for MAP1LC3A Gene - From: DISEASES

Disorder Aliases PubMed IDs
leber congenital amaurosis 6
  • lca6
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MAP1LC3A

genes like me logo Genes that share disorders with MAP1LC3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MAP1LC3A Gene

Publications for MAP1LC3A Gene

  1. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. (PMID: 17580304) Pankiv S … Johansen T (The Journal of biological chemistry 2007) 2 3 4 58
  2. TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. (PMID: 26347139) Kimura T … Deretic V (The Journal of cell biology 2015) 3 4 58
  3. Regulation of endoplasmic reticulum turnover by selective autophagy. (PMID: 26040720) Khaminets A … Dikic I (Nature 2015) 3 4 58
  4. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. (PMID: 24290141) Suzuki H … Wakatsuki S (Structure (London, England : 1993) 2014) 3 4 58
  5. TRIM proteins regulate autophagy and can target autophagic substrates by direct recognition. (PMID: 25127057) Mandell MA … Deretic V (Developmental cell 2014) 3 4 58

Products for MAP1LC3A Gene

Sources for MAP1LC3A Gene

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