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

    Gene ID: 83746, updated on 10-Dec-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 DNA-templated transcription. Predicted to act upstream of or within several processes, including ectoderm development; stem cell differentiation; and stem cell proliferation. Located in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 7.9), testis (RPKM 7.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See L3MBTL2 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41205312..41231271)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (41680250..41706208)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma. Zhong L, et al. Sci Adv, 2023 Nov 24. PMID 37992172, 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. 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
    4. 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
    5. 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

    See all (81) 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)

    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_2024_08

    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

      UniProtKB/TrEMBL
      A0A0S2Z5Q2

    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

      UniProtKB/TrEMBL
      A0A0S2Z5Q2

    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

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

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