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

Gene ID: 84456, updated on 5-Sep-2021

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
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
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Genomic context

See L3MBTL3 in Genome Data Viewer
Location:
6q23.1
Exon count:
30
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (130018581..130141440)
105.20201022 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 transmembrane protein 244 Neighboring gene uncharacterized LOC105378000 Neighboring gene sterile alpha motif domain containing 3 Neighboring gene uncharacterized LOC112267974 Neighboring gene transmembrane protein 200A

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
GeneReviews: Not available
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
GeneReviews: Not available
Many sequence variants affecting diversity of adult human height.
GeneReviews: Not available
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables molecular_function ND
No biological Data available
more info
 
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 erythrocyte maturation IEA
Inferred from Electronic Annotation
more info
 
involved_in granulocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in macrophage differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
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)

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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.

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/Swiss-Prot
    Q96JM7
    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/Swiss-Prot
    Q96JM7
    Related
    ENSP00000357121.2, ENST00000368139.6
  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/Swiss-Prot
    Q96JM7
  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
    Q96JM7
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    130018581..130141440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715576.3XP_006715639.1  lethal(3)malignant brain tumor-like protein 3 isoform X1

    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
  2. XM_011536184.2XP_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
    Q96JM7
    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_011536181.2XP_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
    Q96JM7
    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
  4. XM_011536180.2XP_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
    Q96JM7
    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
  5. XM_006715578.3XP_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
    Q96JM7
    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
  6. XM_011536179.3XP_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
    Q96JM7
    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
  7. XM_005267161.4XP_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
    Q96JM7
    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
  8. XM_011536183.2XP_011534485.1  lethal(3)malignant brain tumor-like protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011534485.1

    UniProtKB/Swiss-Prot
    Q96JM7
    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
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