MAP1LC3A microtubule associated protein 1 light chain 3 alpha [Homo sapiens (human)] - Gene

Summary

Official Symbol: MAP1LC3Aprovided by HGNC
Official Full Name: microtubule associated protein 1 light chain 3 alphaprovided by HGNC
Primary source: HGNC:HGNC:6838
See related: Ensembl:ENSG00000101460 MIM:601242; AllianceGenome:HGNC:6838
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LC3; LC3A; ATG8E; MAP1ALC3; MAP1BLC3
Summary: 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]
Expression: Ubiquitous expression in brain (RPKM 31.2), fat (RPKM 18.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q11.22

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (34546844..34560345)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (36270022..36283500)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (33134648..33148149)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Role of LC3-Associated Phagocytosis Inhibits the Inflammatory Response in Aspergillus fumigatus Keratitis.
Title: The Role of LC3-Associated Phagocytosis Inhibits the Inflammatory Response in Aspergillus fumigatus Keratitis.
Synovial fluid exosome-derived miR-182-5p alleviates osteoarthritis by downregulating TNFAIP8 and promoting autophagy through LC3 signaling.
Title: Synovial fluid exosome-derived miR-182-5p alleviates osteoarthritis by downregulating TNFAIP8 and promoting autophagy through LC3 signaling.
Mitophagy Effects of Protodioscin on Human Osteosarcoma Cells by Inhibition of p38MAPK Targeting NIX/LC3 Axis.
Title: Mitophagy Effects of Protodioscin on Human Osteosarcoma Cells by Inhibition of p38MAPK Targeting NIX/LC3 Axis.
Cytoplasmic Expression of TP53INP2 Modulated by Demethylase FTO and Mutant NPM1 Promotes Autophagy in Leukemia Cells.
Title: Cytoplasmic Expression of TP53INP2 Modulated by Demethylase FTO and Mutant NPM1 Promotes Autophagy in Leukemia Cells.
Nucleophagic Degradation of Progerin Ameliorates Defenestration in Liver Sinusoidal Endothelium Due to SIRT1-Mediated Deacetylation of Nuclear LC3.
Title: Nucleophagic Degradation of Progerin Ameliorates Defenestration in Liver Sinusoidal Endothelium Due to SIRT1-Mediated Deacetylation of Nuclear LC3.
Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer.
Title: Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer.
Tumor cell-released LC3-positive EVs promote lung metastasis of breast cancer through enhancing premetastatic niche formation.
Title: Tumor cell-released LC3-positive EVs promote lung metastasis of breast cancer through enhancing premetastatic niche formation.
IL-6 secretion of CD4(+) T cells stimulated by LC3-positive extracellular vesicles in human epithelial ovarian cancer.
Title: IL-6 secretion of CD4(+) T cells stimulated by LC3-positive extracellular vesicles in human epithelial ovarian cancer.
Human platelets display dysregulated sepsis-associated autophagy, induced by altered LC3 protein-protein interaction of the Vici-protein EPG5.
Title: Human platelets display dysregulated sepsis-associated autophagy, induced by altered LC3 protein-protein interaction of the Vici-protein EPG5.
Role for autophagy-related markers Beclin-1 and LC3 in endometriosis.
Title: Role for autophagy-related markers Beclin-1 and LC3 in endometriosis.

Submit: New GeneRIF Correction See all GeneRIFs (203)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 Env gp120 treatment of SH-SY5Y cells increases MAP1LC3A (LC3-II, membrane-associated lipidated form) which indicates induction of autophagy	PubMed
	env	HIV-1 gp120 downregulates the expression of nucleolin and modulates the expression of LC3, leading to autophage and cell death of uninfected CD4 T cells	PubMed
Nef	nef	HIV-1 Nef-treated mesenchymal stem cells downregulates the conversion of LC3I to LC3II, reflecting a decrease in autophagic efflux in cells	PubMed
Pr55(Gag)	gag	HIV-1 Gag fractionates with the cellular cytosol markers LC3A/B and the plasma membrane marker Na-K ATPase in 293T cells	PubMed
Tat	tat	HIV-1 Tat upregulates MAP1LC3A (LC3-II) levels suggesting increased autophagy in primary rat or human fetal brain tissue	PubMed
Vif	vif	HIV-1 Vif binds more strongly to autophagy-related protein 4 (ATG4)-cleaved form I (LC3-I) than to ATG4-cleaved form II (LC3-II) in an A3G-independent manner	PubMed
	vif	The domain 144-159 inside the SOCS box-like motif of HIV-1 Vif and the glycine 120 of microtubule-associated protein light chain 3 (LC3) are required for the binding between Vif and LC3	PubMed
	vif	GST pull-down assay demonstrates that HIV-1 Vif physically interacts with light chain 3 proteins LC3A, LC3B, and LC3C in HEK cells	PubMed
capsid	gag	HIV-1 CA co-localizes with LC3 in Jurkat cells and primary CD4+ T cells	PubMed
retropepsin	gag-pol	HIV-1 protease extensively cleaves microtubule-associated proteins 1 and 2 and completely inhibits microtubule assembly	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylethanolamine binding	IBA Inferred from Biological aspect of Ancestor more info
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in SMAD protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagosome maturation	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome maturation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within autophagy of mitochondrion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to amino acid starvation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to copper ion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to nitrogen starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to oxygen-glucose deprivation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to starvation	IDA Inferred from Direct Assay more info	PubMed
involved_in macroautophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in mitophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in p38MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in response to iron(II) ion	IEA Inferred from Electronic Annotation more info
involved_in response to lead ion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in autolysosome	IDA Inferred from Direct Assay more info	PubMed
located_in autophagosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in autophagosome membrane	TAS Traceable Author Statement more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in microtubule	IEA Inferred from Electronic Annotation more info
located_in organelle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: microtubule-associated proteins 1A/1B light chain 3A

Names: MAP1 light chain 3-like protein 1; MAP1A/1B light chain 3 A; MAP1A/MAP1B LC3 A; MAP1A/MAP1B light chain 3 A; autophagy-related ubiquitin-like modifier LC3 A; microtubule-associated proteins 1A/1B light chain 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_032514.4 → NP_115903.1 microtubule-associated proteins 1A/1B light chain 3A isoform a

See identical proteins and their annotated locations for NP_115903.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the predominant isoform (a).

Source sequence(s)

AF276658, BP212418, EL954540

Consensus CDS

CCDS13238.1

UniProtKB/Swiss-Prot

E1P5P4, E1P5P5, Q9BXW5, Q9H492

Related

ENSP00000353886.3, ENST00000360668.8

Conserved Domains (1) summary

cd17234
Location:4 → 120

Ubl_ATG8_MAP1LC3A; ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A)
NM_181509.3 → NP_852610.1 microtubule-associated proteins 1A/1B light chain 3A isoform b

See identical proteins and their annotated locations for NP_852610.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1, resulting in an isoform (b) which has a distinct N-terminus compared to isoform a.

Source sequence(s)

AF276658, AL118520, BM740344, BP212418

Consensus CDS

CCDS13237.1

UniProtKB/Swiss-Prot

Q9H492

Related

ENSP00000363970.3, ENST00000374837.7

Conserved Domains (1) summary

cd01611
Location:18 → 124

GABARAP; Ubiquitin domain of GABA-receptor-associated protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

34546844..34560345

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011529084.3 → XP_011527386.1 microtubule-associated proteins 1A/1B light chain 3A isoform X1

See identical proteins and their annotated locations for XP_011527386.1

Conserved Domains (2) summary

cd01611
Location:109 → 222

GABARAP; Ubiquitin domain of GABA-receptor-associated protein

pfam01453
Location:30 → 71

B_lectin; D-mannose binding lectin
XM_011529085.3 → XP_011527387.1 microtubule-associated proteins 1A/1B light chain 3A isoform X2

Conserved Domains (1) summary

cd01611
Location:68 → 181

GABARAP; Ubiquitin domain of GABA-receptor-associated protein
XM_047440559.1 → XP_047296515.1 microtubule-associated proteins 1A/1B light chain 3A isoform X3

UniProtKB/Swiss-Prot

E1P5P4, E1P5P5, Q9BXW5, Q9H492
XM_047440558.1 → XP_047296514.1 microtubule-associated proteins 1A/1B light chain 3A isoform X3

UniProtKB/Swiss-Prot

E1P5P4, E1P5P5, Q9BXW5, Q9H492

Related

ENSP00000380821.1, ENST00000397709.1

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

36270022..36283500

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324144.1 → XP_054180119.1 microtubule-associated proteins 1A/1B light chain 3A isoform X1
XM_054324145.1 → XP_054180120.1 microtubule-associated proteins 1A/1B light chain 3A isoform X2
XM_054324147.1 → XP_054180122.1 microtubule-associated proteins 1A/1B light chain 3A isoform X3

UniProtKB/Swiss-Prot

E1P5P4, E1P5P5, Q9BXW5, Q9H492
XM_054324146.1 → XP_054180121.1 microtubule-associated proteins 1A/1B light chain 3A isoform X3

UniProtKB/Swiss-Prot

E1P5P4, E1P5P5, Q9BXW5, Q9H492