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    L3MBTL3 L3MBTL histone methyl-lysine binding protein 3 [ Homo sapiens (human) ]

    Gene ID: 84456, updated on 10-Dec-2024

    Summary

    Official Symbol
    L3MBTL3provided by HGNC
    Official Full Name
    L3MBTL histone methyl-lysine binding protein 3provided by HGNC
    Primary source
    HGNC:HGNC:23035
    See related
    Ensembl:ENSG00000198945 MIM:618844; AllianceGenome:HGNC:23035
    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
    MBT1; MBT-1
    Summary
    This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of this gene has been observed in human patients with medulloblastoma. [provided by RefSeq, Oct 2016]
    Expression
    Ubiquitous expression in endometrium (RPKM 5.0), spleen (RPKM 4.6) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See L3MBTL3 in Genome Data Viewer
    Location:
    6q23.1
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (130018581..130141438)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (131211018..131336219)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (130339726..130462583)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2 pseudogene 1 Neighboring gene uncharacterized LOC105377999 Neighboring gene Sharpr-MPRA regulatory region 9310 Neighboring gene transmembrane protein 244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25051 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:130267865-130268391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:130280283-130280819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:130280820-130281355 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130290138-130290858 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130322225-130322782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17535 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25055 Neighboring gene NANOG hESC enhancer GRCh37_chr6:130473790-130474410 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:130498512-130498711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:130515807-130516307 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130518767-130519347 Neighboring gene sterile alpha motif domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25059 Neighboring gene uncharacterized LOC112267974 Neighboring gene MPRA-validated peak6122 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17539 Neighboring gene transmembrane protein 200A

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables methylation-dependent protein binding IPI
    Inferred from Physical Interaction
    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
     
    Component Evidence Code Pubs
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    lethal(3)malignant brain tumor-like protein 3
    Names
    H-l(3)mbt-like protein 3
    L3MBTL3, histone methyl-lysine binding protein
    L3mbt-like 3
    l(3)mbt-like 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_051942.1 RefSeqGene

      Range
      5213..128070
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001007102.4NP_001007103.1  lethal(3)malignant brain tumor-like protein 3 isoform b

      See identical proteins and their annotated locations for NP_001007103.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).
      Source sequence(s)
      AB058701, AI123736, AK094137, DA927626, DB059438, DB080397
      Consensus CDS
      CCDS34538.1
      UniProtKB/TrEMBL
      A8K2F4
      Related
      ENSP00000437185.1, ENST00000533560.5
      Conserved Domains (4) summary
      cd09582
      Location:680745
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:680746
      SAM; Sterile alpha motif
      smart00561
      Location:211307
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:532559
      zf-C2HC; Zinc finger, C2HC type
    2. NM_001346550.2NP_001333479.1  lethal(3)malignant brain tumor-like protein 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).
      Source sequence(s)
      AL355581, AL356579, AL583846
      Consensus CDS
      CCDS34538.1
      UniProtKB/TrEMBL
      A8K2F4
    3. NM_001346551.2NP_001333480.1  lethal(3)malignant brain tumor-like protein 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).
      Source sequence(s)
      AL355581, AL356579, AL583846
      Consensus CDS
      CCDS34538.1
      UniProtKB/TrEMBL
      A8K2F4
    4. NM_032438.4NP_115814.1  lethal(3)malignant brain tumor-like protein 3 isoform a

      See identical proteins and their annotated locations for NP_115814.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AL355581, AL356579, AL583846
      Consensus CDS
      CCDS34537.1
      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Related
      ENSP00000354526.2, ENST00000361794.7
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      130018581..130141438
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419407.1XP_047275363.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    2. XM_011536184.3XP_011534486.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011534486.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    3. XM_047419410.1XP_047275366.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    4. XM_006715576.4XP_006715639.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:740805
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:740806
      SAM; Sterile alpha motif
      smart00561
      Location:271367
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:592619
      zf-C2HC; Zinc finger, C2HC type
    5. XM_047419401.1XP_047275357.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    6. XM_047419408.1XP_047275364.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    7. XM_011536181.3XP_011534483.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011534483.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    8. XM_047419400.1XP_047275356.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    9. XM_011536180.3XP_011534482.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011534482.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    10. XM_006715578.4XP_006715641.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006715641.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    11. XM_047419412.1XP_047275368.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    12. XM_047419404.1XP_047275360.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    13. XM_047419405.1XP_047275361.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    14. XM_011536179.4XP_011534481.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011534481.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    15. XM_047419409.1XP_047275365.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
      Related
      ENSP00000436706.1, ENST00000526019.5
    16. XM_005267161.5XP_005267218.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_005267218.1

      UniProtKB/Swiss-Prot
      Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7
      UniProtKB/TrEMBL
      A8K2F4
      Related
      ENSP00000357118.2, ENST00000368136.3
      Conserved Domains (4) summary
      cd09582
      Location:705770
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00454
      Location:705771
      SAM; Sterile alpha motif
      smart00561
      Location:236332
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:557584
      zf-C2HC; Zinc finger, C2HC type
    17. XM_047419403.1XP_047275359.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    18. XM_047419402.1XP_047275358.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      131211018..131336219
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356530.1XP_054212505.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    2. XM_054356537.1XP_054212512.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    3. XM_054356544.1XP_054212519.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    4. XM_054356542.1XP_054212517.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    5. XM_054356547.1XP_054212522.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    6. XM_054356532.1XP_054212507.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    7. XM_054356545.1XP_054212520.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    8. XM_054356538.1XP_054212513.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    9. XM_054356531.1XP_054212506.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    10. XM_054356541.1XP_054212516.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    11. XM_054356543.1XP_054212518.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    12. XM_054356548.1XP_054212523.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    13. XM_054356535.1XP_054212510.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    14. XM_054356536.1XP_054212511.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    15. XM_054356539.1XP_054212514.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    16. XM_054356546.1XP_054212521.1  lethal(3)malignant brain tumor-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A8K2F4
    17. XM_054356540.1XP_054212515.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A8K2F4
    18. XM_054356534.1XP_054212509.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4
    19. XM_054356533.1XP_054212508.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K2F4