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

Gene ID: 84456, updated on 3-Apr-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
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Genomic context

See L3MBTL3 in Genome Data Viewer
Location:
6q23.1
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (130018581..130141438)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (131211018..131336219)
105.20220307 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

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

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)

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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/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_2023_10

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

  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

  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

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

  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

  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

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

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

  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

    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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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