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    L3MBTL1 L3MBTL histone methyl-lysine binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 26013, updated on 10-Dec-2024

    Summary

    Official Symbol
    L3MBTL1provided by HGNC
    Official Full Name
    L3MBTL histone methyl-lysine binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:15905
    See related
    Ensembl:ENSG00000185513 MIM:608802; AllianceGenome:HGNC:15905
    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
    L3MBTL; ZC2HC3; H-L(3)MBT; dJ138B7.3
    Summary
    This gene represents a polycomb group gene. The encoded protein functions to regulate gene activity, likely via chromatin modification. The encoded protein may also be necessary for mitosis. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
    Expression
    Broad expression in testis (RPKM 4.3), brain (RPKM 2.6) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See L3MBTL1 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43507697..43550954)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45240962..45284158)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42136337..42179594)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42086334-42087281 Neighboring gene serine and arginine rich splicing factor 6 Neighboring gene RNA, U6 small nuclear 1251, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12927 Neighboring gene transmembrane protein 14C-like Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42173308-42173524 Neighboring gene serum/glucocorticoid regulated kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42236005-42236846 Neighboring gene intraflagellar transport 52 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42266543-42266756

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (14 hits/1295 screens)

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-08-29)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-08-29)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    General gene information

    Potential readthrough

    Included gene: SGK2

    Clone Names

    • FLJ41181, KIAA0681, DKFZp586P1522

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SAM domain binding PubMed 
    enables chromatin binding  
    enables chromatin binding PubMed 
    enables histone binding  
    enables histone binding PubMed 
    enables identical protein binding PubMed 
    enables methylated histone binding PubMed 
    enables methylated histone binding PubMed 
    enables nucleosome binding PubMed 
    enables protein binding PubMed 
    enables zinc ion binding  
    Component Evidence Code Pubs
    located_in chromatin PubMed 
    part_of chromatin lock complex PubMed 
    located_in condensed chromosome PubMed 
    NOT located_in nucleolus PubMed 
    located_in nucleoplasm PubMed 
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 

    General protein information

    Preferred Names
    lethal(3)malignant brain tumor-like protein 1
    Names
    L3MBTL1, histone methyl-lysine binding protein
    l(3)mbt protein homolog
    l(3)mbt-like 1
    lethal (3) malignant brain tumor l(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_009238.3 RefSeqGene

      Range
      5018..48275
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1049

    mRNA and Protein(s)

    1. NM_001377303.1 → NP_001364232.1  lethal(3)malignant brain tumor-like protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93043.1
      UniProtKB/TrEMBL
      A0A3F2YNZ1, A0A994J4Z1
      Related
      ENSP00000398516.2, ENST00000418998.7
      Conserved Domains (4) summary
      smart00561
      Location:407 → 503
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      PRK07764
      Location:27 → 188
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01530
      Location:643 → 671
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:770 → 798
      SAM_superfamily; SAM (Sterile alpha motif )
    2. NM_001377306.1 → NP_001364235.1  lethal(3)malignant brain tumor-like protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93044.1
      UniProtKB/TrEMBL
      A0A3B3ISS0, A0A994J4Z1
      Related
      ENSP00000497566.1, ENST00000649917.1
      Conserved Domains (4) summary
      smart00561
      Location:407 → 503
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      PRK07764
      Location:27 → 188
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01530
      Location:643 → 671
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:770 → 814
      SAM_superfamily; SAM (Sterile alpha motif )
    3. NM_001377307.1 → NP_001364236.1  lethal(3)malignant brain tumor-like protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      UniProtKB/TrEMBL
      A0A994J4Z1
      Conserved Domains (3) summary
      cd09582
      Location:685 → 750
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:558 → 586
      zf-C2HC; Zinc finger, C2HC type
    4. NM_001377308.1 → NP_001364237.1  lethal(3)malignant brain tumor-like protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93046.1
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000410139.2, ENST00000422861.3
      Conserved Domains (3) summary
      cd09582
      Location:680 → 745
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 581
      zf-C2HC; Zinc finger, C2HC type
    5. NM_001377309.1 → NP_001364238.1  lethal(3)malignant brain tumor-like protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL031681, BC034398, Z98752
      Consensus CDS
      CCDS93045.1
      UniProtKB/TrEMBL
      A0A0A0MRR4, A0A994J4Z1
      Related
      ENSP00000362226.1, ENST00000373134.5
    6. NM_001377310.1 → NP_001364239.1  lethal(3)malignant brain tumor-like protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      UniProtKB/TrEMBL
      A0A994J4Z1
      Conserved Domains (3) summary
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 581
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:680 → 708
      SAM_superfamily; SAM (Sterile alpha motif )
    7. NM_001377311.1 → NP_001364240.1  lethal(3)malignant brain tumor-like protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93047.1
      UniProtKB/TrEMBL
      A0A994J4Z1, B0QYN5
      Related
      ENSP00000415971.2, ENST00000434666.6
      Conserved Domains (3) summary
      cd09582
      Location:640 → 705
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:277 → 373
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:513 → 541
      zf-C2HC; Zinc finger, C2HC type
    8. NM_015478.7 → NP_056293.4  lethal(3)malignant brain tumor-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_056293.4

      Status: REVIEWED

      Source sequence(s)
      AK310345, BC039820, BG956397, BU741824
      Consensus CDS
      CCDS13319.1
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000362227.3, ENST00000373135.8
      Conserved Domains (3) summary
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 579
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:680 → 708
      SAM_superfamily; SAM (Sterile alpha motif )
    9. NM_032107.5 → NP_115479.4  lethal(3)malignant brain tumor-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK299199, BC039820, BG956397, BU741824, DR003568
      Consensus CDS
      CCDS46602.2
      UniProtKB/Swiss-Prot
      B4DRC9, E1P5W7, Q5H8Y8, Q5H8Y9, Q8IUV7, Q9H1E6, Q9H1G5, Q9UG06, Q9UJB9, Q9Y468, Q9Y4C9
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000402107.4, ENST00000427442.8
      Conserved Domains (4) summary
      smart00561
      Location:385 → 481
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:621 → 649
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:748 → 776
      SAM_superfamily; SAM (Sterile alpha motif )
      cl26386
      Location:5 → 166
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    RNA

    1. NR_165189.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
    2. NR_165190.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Related
      ENST00000648570.1
    3. NR_165191.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
    4. NR_165192.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
    5. NR_165193.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
    6. NR_165194.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Related
      ENST00000649501.1
    7. NR_165195.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
    8. NR_165196.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      43507697..43550954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      45240962..45284158
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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