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L3MBTL4 L3MBTL histone methyl-lysine binding protein 4 [ Homo sapiens (human) ]

Gene ID: 91133, updated on 5-Mar-2024

Summary

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Official Symbol
L3MBTL4provided by HGNC
Official Full Name
L3MBTL histone methyl-lysine binding protein 4provided by HGNC
Primary source
HGNC:HGNC:26677
See related
Ensembl:ENSG00000154655 MIM:617135; AllianceGenome:HGNC:26677
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HsT1031
Summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 2.4), ovary (RPKM 1.3) and 24 other tissues See more
Orthologs
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Genomic context

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See L3MBTL4 in Genome Data Viewer
Location:
18p11.31
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (5954717..6415259, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (6114833..6575726, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (5954716..6415258, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene MIR3976 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9264 Neighboring gene microRNA 3976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:5891299-5891826 Neighboring gene uncharacterized LOC121725015 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:5899993-5901192 Neighboring gene transmembrane protein 200C Neighboring gene OCT4 hESC enhancer GRCh37_chr18:5941844-5942352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:5964119-5964619 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:5964978-5965478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13058 Neighboring gene Sharpr-MPRA regulatory region 6254 Neighboring gene RNA, U5F small nuclear 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:6146293-6146793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13059 Neighboring gene L3MBTL4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13060 Neighboring gene uncharacterized LOC124904240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:6382344-6383130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:6383131-6383916 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9267 Neighboring gene microRNA 4317 Neighboring gene RNA, U6 small nuclear 349, pseudogene Neighboring gene ribosomal protein L6 pseudogene 27

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Genome Wide Association Study Identifies L3MBTL4 as a Novel Susceptibility Gene for Hypertension. Liu X, et al. Sci Rep, 2016 Aug 2. PMID 27480026, Free PMC Article
  2. Loss, mutation and deregulation of L3MBTL4 in breast cancers. Addou-Klouche L, et al. Mol Cancer, 2010 Aug 10. PMID 20698951, Free PMC Article
  3. Molecular cloning and chemical synthesis of a region of platelet glycoprotein IIb involved in adhesive function. Loftus JC, et al. Proc Natl Acad Sci U S A, 1987 Oct. PMID 2444974, Free PMC Article
  4. A genome-wide association study of sleep habits and insomnia. Byrne EM, et al. Am J Med Genet B Neuropsychiatr Genet, 2013 Jul. PMID 23728906, Free PMC Article
  5. Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency. Ferreira RC, et al. Nat Genet, 2010 Sep. PMID 20694011

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Findings pinpointed L3MBTL4 as a critical contributor to the development and progression of hypertension.
    Title: Genome Wide Association Study Identifies L3MBTL4 as a Novel Susceptibility Gene for Hypertension.
  2. identified L3MBTL4 as a potential tumor suppressor gene of chromosome arm 18p. The gene is targeted by deletion, breakage and mutations and its mRNA is downregulated in breast tumors
    Title: Loss, mutation and deregulation of L3MBTL4 in breast cancers.
  3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of sleep habits and insomnia.
EBI GWAS Catalog
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding IBA
Inferred from Biological aspect of Ancestor
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 negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
lethal(3)malignant brain tumor-like protein 4
Names
H-l(3)mbt-like protein 4
L3MBTL4, histone methyl-lysine binding protein

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.

mRNA and Protein(s)

  1. NM_001330559.2 → NP_001317488.1  lethal(3)malignant brain tumor-like protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228, CA313345
    Consensus CDS
    CCDS82238.1
    UniProtKB/TrEMBL
    F8W9S8
    Related
    ENSP00000318543.7, ENST00000317931.12
    Conserved Domains (3) summary
    cd09582
    Location:531 → 596
    SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  2. NM_001365765.2 → NP_001352694.1  lethal(3)malignant brain tumor-like protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228
    Consensus CDS
    CCDS82238.1
    UniProtKB/TrEMBL
    F8W9S8
    Conserved Domains (3) summary
    cd09582
    Location:531 → 596
    SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  3. NM_001365766.2 → NP_001352695.1  lethal(3)malignant brain tumor-like protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228
    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  4. NM_001365767.2 → NP_001352696.1  lethal(3)malignant brain tumor-like protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AP001021, AP005060, BC039316
    Consensus CDS
    CCDS92428.1
    Related
    ENSP00000382975.3, ENST00000400104.7
    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  5. NM_001365768.2 → NP_001352697.1  lethal(3)malignant brain tumor-like protein 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228
    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  6. NM_001365769.2 → NP_001352698.1  lethal(3)malignant brain tumor-like protein 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228
    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  7. NM_001365770.2 → NP_001352699.1  lethal(3)malignant brain tumor-like protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AK093255, AP001021
    Consensus CDS
    CCDS11839.2
    UniProtKB/Swiss-Prot
    A8MTL8, Q8IXS3, Q8NA19
    Related
    ENSP00000382976.2, ENST00000400105.6
    Conserved Domains (3) summary
    cd09582
    Location:540 → 605
    SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

  8. NM_173464.4 → NP_775735.2  lethal(3)malignant brain tumor-like protein 4 isoform 1

    See identical proteins and their annotated locations for NP_775735.2

    Status: VALIDATED

    Source sequence(s)
    AK026733, AK093255, CA313345, DB455331
    Consensus CDS
    CCDS11839.2
    UniProtKB/Swiss-Prot
    A8MTL8, Q8IXS3, Q8NA19
    Conserved Domains (3) summary
    cd09582
    Location:540 → 605
    SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 407
    zf-C2HC; Zinc finger, C2HC type

RNA

  1. NR_158609.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228

  2. NR_158610.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228

  3. NR_158611.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP000874, AP001021, AP005060, AP005228

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    5954717..6415259 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437914.1 → XP_047293870.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  2. XM_017026074.2 → XP_016881563.1  lethal(3)malignant brain tumor-like protein 4 isoform X4

  3. XM_011525760.2 → XP_011524062.1  lethal(3)malignant brain tumor-like protein 4 isoform X2

    Conserved Domains (3) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type
    cl15755
    Location:531 → 560
    SAM_superfamily; SAM (Sterile alpha motif )

  4. XM_011525757.2 → XP_011524059.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011524059.1

    Conserved Domains (3) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type
    cl15755
    Location:540 → 569
    SAM_superfamily; SAM (Sterile alpha motif )

  5. XM_047437919.1 → XP_047293875.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  6. XM_011525759.2 → XP_011524061.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011524061.1

    Conserved Domains (3) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type
    cl15755
    Location:540 → 569
    SAM_superfamily; SAM (Sterile alpha motif )

  7. XM_047437917.1 → XP_047293873.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  8. XM_011525758.2 → XP_011524060.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011524060.1

    Conserved Domains (3) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type
    cl15755
    Location:540 → 569
    SAM_superfamily; SAM (Sterile alpha motif )

  9. XM_047437920.1 → XP_047293876.1  lethal(3)malignant brain tumor-like protein 4 isoform X7

  10. XM_047437918.1 → XP_047293874.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  11. XM_047437916.1 → XP_047293872.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  12. XM_047437915.1 → XP_047293871.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  13. XM_011525767.3 → XP_011524069.1  lethal(3)malignant brain tumor-like protein 4 isoform X10

    Conserved Domains (3) summary
    smart00561
    Location:1 → 75
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:90 → 116
    zf-C2HC; Zinc finger, C2HC type
    cl15755
    Location:251 → 280
    SAM_superfamily; SAM (Sterile alpha motif )

  14. XM_011525762.3 → XP_011524064.1  lethal(3)malignant brain tumor-like protein 4 isoform X5

    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type

  15. XM_006722364.3 → XP_006722427.1  lethal(3)malignant brain tumor-like protein 4 isoform X8

    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type

  16. XM_011525763.3 → XP_011524065.1  lethal(3)malignant brain tumor-like protein 4 isoform X6

    Conserved Domains (2) summary
    smart00561
    Location:273 → 364
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam01530
    Location:379 → 405
    zf-C2HC; Zinc finger, C2HC type

  17. XM_017026077.2 → XP_016881566.1  lethal(3)malignant brain tumor-like protein 4 isoform X9

RNA

  1. XR_007066253.1 RNA Sequence

  2. XR_935072.2 RNA Sequence

  3. XR_007066252.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    6114833..6575726 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319328.1 → XP_054175303.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  2. XM_054319337.1 → XP_054175312.1  lethal(3)malignant brain tumor-like protein 4 isoform X4

  3. XM_054319333.1 → XP_054175308.1  lethal(3)malignant brain tumor-like protein 4 isoform X2

  4. XM_054319327.1 → XP_054175302.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  5. XM_054319336.1 → XP_054175311.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  6. XM_054319332.1 → XP_054175307.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  7. XM_054319334.1 → XP_054175309.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  8. XM_054319329.1 → XP_054175304.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  9. XM_054319340.1 → XP_054175315.1  lethal(3)malignant brain tumor-like protein 4 isoform X7

  10. XM_054319335.1 → XP_054175310.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

    UniProtKB/TrEMBL
    F8W9S8

  11. XM_054319331.1 → XP_054175306.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  12. XM_054319330.1 → XP_054175305.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

  13. XM_054319343.1 → XP_054175318.1  lethal(3)malignant brain tumor-like protein 4 isoform X10

  14. XM_054319338.1 → XP_054175313.1  lethal(3)malignant brain tumor-like protein 4 isoform X5

  15. XM_054319341.1 → XP_054175316.1  lethal(3)malignant brain tumor-like protein 4 isoform X8

  16. XM_054319339.1 → XP_054175314.1  lethal(3)malignant brain tumor-like protein 4 isoform X6

  17. XM_054319342.1 → XP_054175317.1  lethal(3)malignant brain tumor-like protein 4 isoform X9

RNA

  1. XR_008485033.1 RNA Sequence

  2. XR_008485034.1 RNA Sequence

  3. XR_008485032.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NA19.2 GenPept UniProtKB/Swiss-Prot:Q8NA19

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