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Aliases for L3MBTL1 Gene

Aliases for L3MBTL1 Gene

  • L3MBTL1, Histone Methyl-Lysine Binding Protein 2 3 5
  • Lethal (3) Malignant Brain Tumor L(3) 2 3
  • L(3)Mbt Protein Homolog 3 4
  • L3MBTL 3 4
  • Lethal(3)Malignant Brain Tumor-Like Protein 1 3
  • L(3)Mbt-Like 1 (Drosophila) 2
  • L(3)Mbt (Drosophila)-Like 2
  • L(3)Mbt-Like (Drosophila) 2
  • H-L(3)Mbt Protein 4
  • L(3)Mbt-Like 1 3
  • L(3)Mbt-Like 4
  • H-L(3)MBT 3
  • DJ138B7.3 3
  • H-L(3)Mbt 4
  • KIAA0681 4
  • ZC2HC3 3
  • L3MBT 4

External Ids for L3MBTL1 Gene

Previous HGNC Symbols for L3MBTL1 Gene

  • L3MBTL

Previous GeneCards Identifiers for L3MBTL1 Gene

  • GC20P038878
  • GC20P042137

Summaries for L3MBTL1 Gene

Entrez Gene Summary for L3MBTL1 Gene

  • 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]

GeneCards Summary for L3MBTL1 Gene

L3MBTL1 (L3MBTL1, Histone Methyl-Lysine Binding Protein) is a Protein Coding gene. Diseases associated with L3MBTL1 include Shwachman-Diamond Syndrome 1 and Brain Cancer. Among its related pathways are Gene Expression and Regulation of TP53 Activity. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is L3MBTL3.

UniProtKB/Swiss-Prot for L3MBTL1 Gene

  • Polycomb group (PcG) protein that specifically recognizes and binds mono- and dimethyllysine residues on target proteins, therey acting as a reader of a network of post-translational modifications. PcG proteins maintain the transcriptionally repressive state of genes: acts as a chromatin compaction factor by recognizing and binding mono- and dimethylated histone H1b/HIST1H1E at Lys-26 (H1bK26me1 and H1bK26me2) and histone H4 at Lys-20 (H4K20me1 and H4K20me2), leading to condense chromatin and repress transcription. Recognizes and binds p53/TP53 monomethylated at Lys-382, leading to repress p53/TP53-target genes. Also recognizes and binds RB1/RB monomethylated at Lys-860. Participates in the ETV6-mediated repression. Probably plays a role in cell proliferation. Overexpression induces multinucleated cells, suggesting that it is required to accomplish normal mitosis.

Tocris Summary for L3MBTL1 Gene

Gene Wiki entry for L3MBTL1 Gene

Additional gene information for L3MBTL1 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for L3MBTL1 Gene

Genomics for L3MBTL1 Gene

GeneHancer (GH) Regulatory Elements for L3MBTL1 Gene

Promoters and enhancers for L3MBTL1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J043513 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.4 +6.8 6791 2.3 HDGF PKNOX1 ARID4B DMAP1 ZNF2 YY1 ZNF121 GLIS2 ZNF143 ATF7 L3MBTL1 RNU6-1251P ENSG00000226143 IFT52 SGK2 ENSG00000234271 GC20M043507
GH20J043507 Promoter/Enhancer 1.4 Ensembl ENCODE 650.7 +0.6 606 1.4 ZFP64 ARID4B SIN3A DMAP1 ZNF48 GTF3C2 GLIS2 ZNF202 SP3 MXD4 L3MBTL1 SRSF6 ENSG00000234271 GC20M043507
GH20J043456 Promoter/Enhancer 2.5 UCNEbase EPDnew Ensembl ENCODE 28.4 -49.5 -49464 3.4 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 SP3 NFYC SRSF6 L3MBTL1 IFT52 RPL27AP ENSG00000237555 LINC01728 LOC101927138 OSER1 GC20P043474
GH20J044173 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.8 +674.1 674106 15.7 HDGF PKNOX1 MLX YBX1 DMAP1 ZNF48 TCF12 ZNF121 ZNF207 MCM5 JPH2 SRSF6 OSER1 L3MBTL1 FITM2 IFT52 SGK2 OSER1-DT GC20P044130
GH20J044206 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.7 +702.2 702209 6.1 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 OSER1 OSER1-DT SRSF6 IFT52 RPL27AP LINC01728 ENSG00000237555 FITM2 L3MBTL1 KCNK15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around L3MBTL1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for L3MBTL1 Gene

Genomic Locations for L3MBTL1 Gene
chr20:43,507,680-43,550,950
(GRCh38/hg38)
Size:
43,271 bases
Orientation:
Plus strand
chr20:42,136,320-42,179,590
(GRCh37/hg19)

Genomic View for L3MBTL1 Gene

Genes around L3MBTL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
L3MBTL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for L3MBTL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for L3MBTL1 Gene

Proteins for L3MBTL1 Gene

  • Protein details for L3MBTL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y468-LMBL1_HUMAN
    Recommended name:
    Lethal(3)malignant brain tumor-like protein 1
    Protein Accession:
    Q9Y468
    Secondary Accessions:
    • B4DRC9
    • E1P5W7
    • Q5H8Y8
    • Q5H8Y9
    • Q8IUV7
    • Q9H1E6
    • Q9H1G5
    • Q9UG06
    • Q9UJB9
    • Q9Y4C9

    Protein attributes for L3MBTL1 Gene

    Size:
    840 amino acids
    Molecular mass:
    92297 Da
    Quaternary structure:
    • Homodimer. Interacts with RB1/RB (when monomethylated at Lys-860). Interacts with p53/TP53 (when monomethylated at Lys-382). Interacts with CBX3, ETV6, KMT5A and VCP/p97.
    Miscellaneous:
    • The L3MBTL1 locus is imprinted. Paternal inherited gene is expressed, while the maternal inherited gene is silenced.
    SequenceCaution:
    • Sequence=EAW75958.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAW75961.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAW75962.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for L3MBTL1 Gene

    Alternative splice isoforms for L3MBTL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for L3MBTL1 Gene

Post-translational modifications for L3MBTL1 Gene

  • Ubiquitinated in a VCP/p97-dependent way following DNA damage, leading to its removal from DNA damage sites, promoting accessibility of H4K20me2 mark for DNA repair protein TP53BP1, which is then recruited to DNA damage sites.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for L3MBTL1 Gene

Domains & Families for L3MBTL1 Gene

Gene Families for L3MBTL1 Gene

Protein Domains for L3MBTL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for L3MBTL1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y468

UniProtKB/Swiss-Prot:

LMBL1_HUMAN :
  • The MBT repeat 2 specifically recognizes and binds monomethylated and dimethylated proteins. In contrast, it does not bind trimethylated proteins. The MBT repeat 1 does not bind methylated peptides but inserts a proline ring in a Pro-Ser-Ser/Thr sequence context.
Domain:
  • The MBT repeat 2 specifically recognizes and binds monomethylated and dimethylated proteins. In contrast, it does not bind trimethylated proteins. The MBT repeat 1 does not bind methylated peptides but inserts a proline ring in a Pro-Ser-Ser/Thr sequence context.
genes like me logo Genes that share domains with L3MBTL1: view

Function for L3MBTL1 Gene

Molecular function for L3MBTL1 Gene

UniProtKB/Swiss-Prot Function:
Polycomb group (PcG) protein that specifically recognizes and binds mono- and dimethyllysine residues on target proteins, therey acting as a reader of a network of post-translational modifications. PcG proteins maintain the transcriptionally repressive state of genes: acts as a chromatin compaction factor by recognizing and binding mono- and dimethylated histone H1b/HIST1H1E at Lys-26 (H1bK26me1 and H1bK26me2) and histone H4 at Lys-20 (H4K20me1 and H4K20me2), leading to condense chromatin and repress transcription. Recognizes and binds p53/TP53 monomethylated at Lys-382, leading to repress p53/TP53-target genes. Also recognizes and binds RB1/RB monomethylated at Lys-860. Participates in the ETV6-mediated repression. Probably plays a role in cell proliferation. Overexpression induces multinucleated cells, suggesting that it is required to accomplish normal mitosis.

Phenotypes From GWAS Catalog for L3MBTL1 Gene

Gene Ontology (GO) - Molecular Function for L3MBTL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 18408754
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 12588862
GO:0008270 zinc ion binding IEA --
GO:0031491 nucleosome binding IDA 17540172
genes like me logo Genes that share ontologies with L3MBTL1: view
genes like me logo Genes that share phenotypes with L3MBTL1: view

Animal Models for L3MBTL1 Gene

MGI Knock Outs for L3MBTL1:

Animal Model Products

miRNA for L3MBTL1 Gene

miRTarBase miRNAs that target L3MBTL1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for L3MBTL1 Gene

Localization for L3MBTL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for L3MBTL1 Gene

Nucleus. Note=Excluded from the nucleolus. Does not colocalizes with the PcG protein BMI1, suggesting that these two proteins do not belong to the same complex.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for L3MBTL1 gene
Compartment Confidence
plasma membrane 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for L3MBTL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 18408754
GO:0000793 condensed chromosome IDA 10445843
GO:0005634 nucleus IDA 10445843
GO:0005654 nucleoplasm TAS --
GO:0005730 NOT nucleolus IDA 10445843
genes like me logo Genes that share ontologies with L3MBTL1: view

Pathways & Interactions for L3MBTL1 Gene

genes like me logo Genes that share pathways with L3MBTL1: view

Gene Ontology (GO) - Biological Process for L3MBTL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IDA,IEA 17540172
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007088 regulation of mitotic nuclear division IMP 10445843
GO:0030097 hemopoiesis IEP 15334543
genes like me logo Genes that share ontologies with L3MBTL1: view

No data available for SIGNOR curated interactions for L3MBTL1 Gene

Drugs & Compounds for L3MBTL1 Gene

(2) Drugs for L3MBTL1 Gene - From: DrugBank and ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
2-(N-Morpholino)-Ethanesulfonic Acid Experimental Pharma Target 0
UNC669 Pharma L3MBTL antagonist,potent and selective 0

(2) Additional Compounds for L3MBTL1 Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
UNC 1215
UNC 926 hydrochloride
1184136-10-4

(2) Tocris Compounds for L3MBTL1 Gene

Compound Action Cas Number
UNC 1215 Potent inhibitor of L3MBTL3 Kme reader domain; cell permeable
UNC 926 hydrochloride L3MBTL1 domain inhibitor 1184136-10-4

(1) ApexBio Compounds for L3MBTL1 Gene

Compound Action Cas Number
UNC669 L3MBTL antagonist,potent and selective 1314241-44-5
genes like me logo Genes that share compounds with L3MBTL1: view

Drug Products

Transcripts for L3MBTL1 Gene

mRNA/cDNA for L3MBTL1 Gene

Unigene Clusters for L3MBTL1 Gene

L(3)mbt-like 1 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for L3MBTL1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a ·
SP1: - - - -
SP2: - - -
SP3:
SP4: - - -
SP5: - - - - - -
SP6: - - - -
SP7:
SP8: -
SP9:

ExUns: 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for L3MBTL1 Gene

GeneLoc Exon Structure for
L3MBTL1
ECgene alternative splicing isoforms for
L3MBTL1

Expression for L3MBTL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for L3MBTL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for L3MBTL1 Gene



NURSA nuclear receptor signaling pathways regulating expression of L3MBTL1 Gene:

L3MBTL1

SOURCE GeneReport for Unigene cluster for L3MBTL1 Gene:

Hs.709356

mRNA Expression by UniProt/SwissProt for L3MBTL1 Gene:

Q9Y468-LMBL1_HUMAN
Tissue specificity: Widely expressed. Expression is reduced in colorectal cancer cell line SW480 and promyelocytic leukemia cell line HL-60.

Evidence on tissue expression from TISSUES for L3MBTL1 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with L3MBTL1: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for L3MBTL1 Gene

Orthologs for L3MBTL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for L3MBTL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia L3MBTL1 34 33
  • 99.68 (n)
OneToOne
dog
(Canis familiaris)
Mammalia L3MBTL1 34 33
  • 89.06 (n)
OneToOne
cow
(Bos Taurus)
Mammalia L3MBTL1 33
  • 88.83 (n)
rat
(Rattus norvegicus)
Mammalia L3mbtl1 33
  • 83.66 (n)
mouse
(Mus musculus)
Mammalia L3mbtl1 16 34 33
  • 83.42 (n)
oppossum
(Monodelphis domestica)
Mammalia L3MBTL1 34
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia L3MBTL1 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves L3MBTL1 34 33
  • 71.29 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia L3MBTL1 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia l3mbtl1 33
  • 65.72 (n)
zebrafish
(Danio rerio)
Actinopterygii l3mbtl1 33
  • 61.52 (n)
l3mbtl1a 34
  • 52 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta l(3)mbt 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
OneToMany
Species where no ortholog for L3MBTL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for L3MBTL1 Gene

ENSEMBL:
Gene Tree for L3MBTL1 (if available)
TreeFam:
Gene Tree for L3MBTL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for L3MBTL1: view image

Paralogs for L3MBTL1 Gene

Paralogs for L3MBTL1 Gene

(7) SIMAP similar genes for L3MBTL1 Gene using alignment to 4 proteins:

  • LMBL1_HUMAN
  • B0QYN4_HUMAN
  • B0QYN5_HUMAN
  • H0Y7I2_HUMAN
genes like me logo Genes that share paralogs with L3MBTL1: view

Variants for L3MBTL1 Gene

Sequence variations from dbSNP and Humsavar for L3MBTL1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000122837 -- 43,520,352(+) A/G intron_variant
rs1000128782 -- 43,524,810(+) A/G intron_variant
rs1000375826 -- 43,515,479(+) C/T intron_variant
rs1000384666 -- 43,520,693(+) C/A/T intron_variant
rs1000491880 -- 43,514,212(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for L3MBTL1 Gene

Variant ID Type Subtype PubMed ID
nsv1057847 CNV loss 25217958

Variation tolerance for L3MBTL1 Gene

Residual Variation Intolerance Score: 80.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.34; 53.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for L3MBTL1 Gene

Human Gene Mutation Database (HGMD)
L3MBTL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
L3MBTL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for L3MBTL1 Gene

Disorders for L3MBTL1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for L3MBTL1 Gene - From: HGMD, DISEASES, and Novoseek

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
brain cancer
  • adult brain tumor
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for L3MBTL1

genes like me logo Genes that share disorders with L3MBTL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for L3MBTL1 Gene

Publications for L3MBTL1 Gene

  1. A human homolog of Drosophila lethal(3)malignant brain tumor (l(3)mbt) protein associates with condensed mitotic chromosomes. (PMID: 10445843) Koga H … Saya H (Oncogene 1999) 2 3 4 22 58
  2. L3MBTL1, a histone-methylation-dependent chromatin lock. (PMID: 17540172) Trojer P … Reinberg D (Cell 2007) 2 3 4 58
  3. The human L(3)MBT polycomb group protein is a transcriptional repressor and interacts physically and functionally with TEL (ETV6). (PMID: 12588862) Boccuni P … Nimer SD (The Journal of biological chemistry 2003) 3 4 22 58
  4. The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks. (PMID: 22120668) Acs K … Dantuma NP (Nature structural & molecular biology 2011) 3 4 58
  5. Methylation of the retinoblastoma tumor suppressor by SMYD2. (PMID: 20870719) Saddic LA … Sage J (The Journal of biological chemistry 2010) 3 4 58

Products for L3MBTL1 Gene

Sources for L3MBTL1 Gene

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