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MAP1LC3B microtubule associated protein 1 light chain 3 beta [ Homo sapiens (human) ]

Gene ID: 81631, updated on 3-Nov-2024

Summary

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Official Symbol
MAP1LC3Bprovided by HGNC
Official Full Name
microtubule associated protein 1 light chain 3 betaprovided by HGNC
Primary source
HGNC:HGNC:13352
See related
Ensembl:ENSG00000140941 MIM:609604; AllianceGenome:HGNC:13352
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
LC3B; ATG8F; MAP1LC3B-a; MAP1A/1BLC3
Summary
The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 94.3), brain (RPKM 58.8) and 25 other tissues See more
Orthologs
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Genomic context

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See MAP1LC3B in Genome Data Viewer
Location:
16q24.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (87392336..87404774)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (93463228..93475656)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (87425942..87438380)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene C16orf95 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87364853-87365354 Neighboring gene F-box protein 31 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87379751-87380306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87380307-87380861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87386425-87386966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:87399801-87400302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87403399-87404245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7833 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:87417185-87417838 Neighboring gene uncharacterized LOC124903747 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:87417839-87418490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11321 Neighboring gene tRNA-Met (anticodon CAT) 6-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:87424900-87425858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11322 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:87440788-87441987 Neighboring gene zinc finger CCHC-type containing 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87456781-87457290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87457291-87457798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87458817-87459326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87460343-87460850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87468667-87469584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87486642-87487142 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:87490779-87491978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87502852-87503437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87503438-87504022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87504708-87505665 Neighboring gene nuclear receptor subfamily 3 group C member 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7838 Neighboring gene ZCCHC14 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. High expression of LC3B is associated with progression and poor outcome in triple-negative breast cancer. Zhao H, et al. Med Oncol, 2013 Mar. PMID 23371253
  2. Cell death induced by the ER stressor thapsigargin involves death receptor 5, a non-autophagic function of MAP1LC3B, and distinct contributions from unfolded protein response components. Lindner P, et al. Cell Commun Signal, 2020 Jan 27. PMID 31987044, Free PMC Article
  3. Autophagic LC3B overexpression correlates with malignant progression and predicts a poor prognosis in hepatocellular carcinoma. Wu DH, et al. Tumour Biol, 2014 Dec. PMID 25256671
  4. Differences in LC3B expression and prognostic implications in oropharyngeal and oral cavity squamous cell carcinoma patients. Lai K, et al. BMC Cancer, 2018 Jun 1. PMID 29859041, Free PMC Article
  5. Functional variants in the LC3B gene promoter in acute myocardial infarction. Gao F, et al. J Cell Biochem, 2018 Sep. PMID 29761913

See all (300) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LC3B drives transcription-associated homologous recombination via direct interaction with R-loops.
    Title: LC3B drives transcription-associated homologous recombination via direct interaction with R-loops.
  2. Linc00673-V3 positively regulates autophagy by promoting Smad3-mediated LC3B transcription in NSCLC.
    Title: Linc00673-V3 positively regulates autophagy by promoting Smad3-mediated LC3B transcription in NSCLC.
  3. Identifying CTH and MAP1LC3B as ferroptosis biomarkers for prognostic indication in gastric cancer decoding.
    Title: Identifying CTH and MAP1LC3B as ferroptosis biomarkers for prognostic indication in gastric cancer decoding.
  4. Immunohistochemical Expression of Autophagy-Related Marker (LC3B) and Stem Cell Marker (CD44) in Molecular Subtypes of Breast Cancer.
    Title: Immunohistochemical Expression of Autophagy-Related Marker (LC3B) and Stem Cell Marker (CD44) in Molecular Subtypes of Breast Cancer.
  5. LC3B is lipidated to large lipid droplets during prolonged starvation for noncanonical autophagy.
    Title: LC3B is lipidated to large lipid droplets during prolonged starvation for noncanonical autophagy.
  6. Alterations of ATG4A and LC3B in neurons derived from Alzheimer's disease patients.
    Title: Alterations of ATG4A and LC3B in neurons derived from Alzheimer's disease patients.
  7. Superenhancers activate the autophagy-related genes Beclin1 and LC3B to drive metastasis and drug resistance in osteosarcoma.
    Title: Superenhancers activate the autophagy-related genes Beclin1 and LC3B to drive metastasis and drug resistance in osteosarcoma.
  8. SQSTM1 and its MAP1LC3B-binding domain induce forced mitophagy to degrade mitochondrial carryover during mitochondrial replacement therapy.
    Title: SQSTM1 and its MAP1LC3B-binding domain induce forced mitophagy to degrade mitochondrial carryover during mitochondrial replacement therapy.
  9. [Expression and significance of microtubule associated protein 1 light chain 3B, p62 and Beclin1 in lesion tissues of oral lichen planus patients].
    Title: [Expression and significance of microtubule associated protein 1 light chain 3B, p62 and Beclin1 in lesion tissues of oral lichen planus patients].
  10. The effect of MiR-497 on the expression of target genes BCL-2 and LC3B on cardiomyocytes injured by hypoxia/reoxygenation.
    Title: The effect of MiR-497 on the expression of target genes BCL-2 and LC3B on cardiomyocytes injured by hypoxia/reoxygenation.
Submit: New GeneRIF Correction See all GeneRIFs (119)

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

EBI GWAS Catalog

Description
A mega-analysis of genome-wide association studies for major depressive disorder.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Asp asp ASP interacts and colocalizes with LC3b in a punctate manner in COS-7 cells PubMed
asp HIV-1 ASP expression upregulates the levels of two autophagy markers, LC3b and Beclin 1 in COS-7 cells, suggesting ASP activates autophagy in mammalian cells PubMed
Envelope surface glycoprotein gp120 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
Envelope surface glycoprotein gp160, precursor env HIV-1 Env-mediated autophagy induces upregulation of LC3B expression in CD4/X4 HEK 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
gag Protein/protein interactions of virus/autophagy-associated proteins by yeast two-hybrid array reveals the interaction between HIV-1 Gag and microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) PubMed
Tat tat HIV-1 Tat co-localizes with microtubule-associated protein 1 light chain 3 beta in neuronal cells PubMed
tat HIV-1 Tat downregulates microtubule-associated protein 1 light chain 3 beta levels in a dose-dependent manner in neuronal cells PubMed
tat HIV-1 Tat upregulates the levels of BAG3 in human glioblastoma cells, and BAG3 silencing results in highly reducing Tat-induced upregulation of LC3-II and increasing the appearance of sub G0/G1 apoptotic cells PubMed
tat HIV-1 Tat suppresses IFN-gamma-induced LC3B protein expression and autophagosome formation through Tat-mediated suppression of STAT1 phosphorylation 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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ceramide binding IDA
Inferred from Direct Assay
more info
 PubMed 
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 phosphatidylethanolamine 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 autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
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 
involved_in autophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to nitrogen starvation IBA
Inferred from Biological aspect of Ancestor
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 mitophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitophagy IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in autophagosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in autophagosome ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
is_active_in autophagosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in autophagosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in autophagosome membrane TAS
Traceable Author Statement
more info
  
located_in axoneme ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endomembrane system IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in microtubule IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in organelle membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
microtubule-associated proteins 1A/1B light chain 3B
Names
MAP1 light chain 3-like protein 2
MAP1A/MAP1B LC3 B
MAP1A/MAP1B light chain 3 B
autophagy-related ubiquitin-like modifier LC3 B

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.

Genomic

  1. NG_029030.2 RefSeqGene

    Range
    5002..17440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_022818.5 → NP_073729.1  microtubule-associated proteins 1A/1B light chain 3B

    See identical proteins and their annotated locations for NP_073729.1

    Status: REVIEWED

    Source sequence(s)
    AC010531
    Consensus CDS
    CCDS10960.1
    UniProtKB/Swiss-Prot
    Q6NW02, Q9GZQ8
    UniProtKB/TrEMBL
    Q658J6
    Related
    ENSP00000268607.5, ENST00000268607.10
    Conserved Domains (1) summary
    cd17235
    Location:5 → 119
    Ubl_ATG8_MAP1LC3B; ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3B (MAP1LC3B)

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

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    87392336..87404774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    93463228..93475656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZQ8.3 GenPept UniProtKB/Swiss-Prot:Q9GZQ8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
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