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L3MBTL2 L3MBTL histone methyl-lysine binding protein 2 [ Homo sapiens (human) ]

Gene ID: 83746, updated on 3-Apr-2024

Summary

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Official Symbol
L3MBTL2provided by HGNC
Official Full Name
L3MBTL histone methyl-lysine binding protein 2provided by HGNC
Primary source
HGNC:HGNC:18594
See related
Ensembl:ENSG00000100395 MIM:611865; AllianceGenome:HGNC:18594
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
L3MBT; H-l(3)mbt-l
Summary
Enables methylated histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including ectoderm development; regulation of histone modification; and stem cell proliferation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 7.9), testis (RPKM 7.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q13.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41205312..41231271)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (41680250..41706208)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (41601316..41627275)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene E1A binding protein p300 Neighboring gene RNA, U6 small nuclear 375, pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41580503-41581302 Neighboring gene EP300 antisense RNA 1 Neighboring gene leucine rich repeat containing 37 member A14, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41593165-41593664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19108 Neighboring gene uncharacterized LOC646927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41602160-41602660 Neighboring gene L3MBTL2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41613805-41614502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41614503-41615199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41632734-41633322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41633323-41633911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41633912-41634500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41634501-41635088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41636538-41637038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41637039-41637539 Neighboring gene chondroadherin like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41652381-41652924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41652925-41653468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41654013-41654555 Neighboring gene Ran GTPase activating protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41660124-41660999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41667991-41668491 Neighboring gene microRNA 6889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19112 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41685594-41686193 Neighboring gene Sharpr-MPRA regulatory region 14092 Neighboring gene Sharpr-MPRA regulatory region 10804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13783 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41697637-41698138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41704361-41704862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41704863-41705362 Neighboring gene zinc finger CCCH-type containing 7B Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41720150-41720650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41756000-41756522

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
  • 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. Solution structure of the FCS zinc finger domain of the human polycomb group protein L(3)mbt-like 2. Lechtenberg BC, et al. Protein Sci, 2009 Mar. PMID 19241375, Free PMC Article
  2. Molecular characterization of h-l(3)mbt-like: a new member of the human mbt family. Wismar J. FEBS Lett, 2001 Oct 19. PMID 11682070
  3. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Guo Y, et al. Nucleic Acids Res, 2009 Apr. PMID 19233876, Free PMC Article
  4. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. Nowsheen S, et al. Nat Cell Biol, 2018 Apr. PMID 29581593, Free PMC Article
  5. Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders. Lo MT, et al. Nat Genet, 2017 Jan. PMID 27918536, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma.
    Title: Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma.
  2. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage, regulating the DNA damage response pathway.
    Title: L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage.
  3. L3MBTL2 polymorphism is associated with neuroticism.
    Title: Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders.
  4. Our findings highlight a PcG/L3MBTL2 collaboration that attains repressive chromatin without entailing histone lysine methylation marks.
    Title: L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure.
  5. determination of the solution structure of the FCS zinc finger of L3MBTL2; structure consists of a beta-hairpin followed by an alpha-helix; structure is consistent with the proposal that FCS zinc fingers bind to regulatory RNAs
    Title: Solution structure of the FCS zinc finger domain of the human polycomb group protein L(3)mbt-like 2.
  6. High-resolution crystallographic analysis of the four MBT repeats of L3MBTL2 reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides.
    Title: Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
Submit: New GeneRIF Correction

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
Biological insights from 108 schizophrenia-associated genetic loci.
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

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 chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
lethal(3)malignant brain tumor-like protein 2
Names
H-l(3)mbt-like protein 2
L(3)mbt-like protein 2
L3MBTL2, polycomb repressive complex 1 subunit
l(3)mbt-like 2

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)

  1. NM_031488.5 → NP_113676.2  lethal(3)malignant brain tumor-like protein 2

    See identical proteins and their annotated locations for NP_113676.2

    Status: VALIDATED

    Source sequence(s)
    AJ305226, AJ305227, AK097052, BU184979
    Consensus CDS
    CCDS14011.1
    UniProtKB/Swiss-Prot
    Q8TEN1, Q969R5, Q96SC4, Q9BQI2, Q9UGS4
    UniProtKB/TrEMBL
    A0A0S2Z5X6, B3KPJ8
    Related
    ENSP00000216237.5, ENST00000216237.10
    Conserved Domains (1) summary
    smart00561
    Location:511 → 604
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    41205312..41231271
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028976.2 → XP_016884465.1  lethal(3)malignant brain tumor-like protein 2 isoform X2

  2. XM_047441536.1 → XP_047297492.1  lethal(3)malignant brain tumor-like protein 2 isoform X1

  3. XM_047441537.1 → XP_047297493.1  lethal(3)malignant brain tumor-like protein 2 isoform X4

  4. XM_017028977.2 → XP_016884466.1  lethal(3)malignant brain tumor-like protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    41680250..41706208
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326000.1 → XP_054181975.1  lethal(3)malignant brain tumor-like protein 2 isoform X2

  2. XM_054325999.1 → XP_054181974.1  lethal(3)malignant brain tumor-like protein 2 isoform X1

  3. XM_054326002.1 → XP_054181977.1  lethal(3)malignant brain tumor-like protein 2 isoform X4

  4. XM_054326001.1 → XP_054181976.1  lethal(3)malignant brain tumor-like protein 2 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001003689.1: Suppressed sequence

    Description
    NM_001003689.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969R5.1 GenPept UniProtKB/Swiss-Prot:Q969R5

Gene LinkOut

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