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    MSL3 MSL complex subunit 3 [ Homo sapiens (human) ]

    Gene ID: 10943, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MSL3provided by HGNC
    Official Full Name
    MSL complex subunit 3provided by HGNC
    Primary source
    HGNC:HGNC:7370
    See related
    Ensembl:ENSG00000005302 MIM:300609; AllianceGenome:HGNC:7370
    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
    MRSXBA; MRXS36; MRXSBA; MSL3L1
    Summary
    This gene encodes a nuclear protein that is similar to the product of the Drosophila male-specific lethal-3 gene. The Drosophila protein plays a critical role in a dosage-compensation pathway, which equalizes X-linked gene expression in males and females. Thus, the human protein is thought to play a similar function in chromatin remodeling and transcriptional regulation, and it has been found as part of a complex that is responsible for histone H4 lysine-16 acetylation. This gene can undergo X inactivation. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2, 7 and 8. [provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in lymph node (RPKM 13.7), appendix (RPKM 11.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MSL3 in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (11758159..11775772)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (11340708..11358321)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (11776278..11793891)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20661 Neighboring gene Sharpr-MPRA regulatory region 2065 Neighboring gene MSL3 divergent transcript Neighboring gene FERM and PDZ domain containing 4 Neighboring gene MPRA-validated peak7357 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:12327767-12328270 Neighboring gene FRMPD4 antisense RNA 1 Neighboring gene ribosomal protein L17 pseudogene 49

    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 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. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Brunet T, et al. Genet Med, 2021 Feb. PMID 33173220, Free PMC Article
    2. Characterization of a novel chromo domain gene in xp22.3 with homology to Drosophila msl-3. Prakash SK, et al. Genomics, 1999 Jul 1. PMID 10395802
    3. Disruption of the MSL complex inhibits tumour maintenance by exacerbating chromosomal instability. Monserrat J, et al. Nat Cell Biol, 2021 Apr. PMID 33837287, Free PMC Article
    4. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Basilicata MF, et al. Nat Genet, 2018 Oct. PMID 30224647, Free PMC Article
    5. Origin and evolution of the regulatory gene male-specific lethal-3. Marín I, et al. Mol Biol Evol, 2000 Aug. PMID 10908644

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder.
      Title: Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder.
    2. Characterization of syndrome that allowed us to decipher the developmental importance of MSL3 in humans.
      Title: De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation.
    3. MSL3 plays an important role in targeting the male specific lethal complex to chromatin in both humans and flies by binding to H4K20Me(1).
      Title: Structural and biochemical studies on the chromo-barrel domain of male specific lethal 3 (MSL3) reveal a binding preference for mono- or dimethyllysine 20 on histone H4.
    4. A multisubunit human histone acetylase complex that contains homologs of the Drosophila MSL proteins MOF, MSL1 (hampin A), MSL2, and MSL3 was described. This complex is responsible for histone H4 lysine-16 acetylation of all cellular chromosomes.
      Title: A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16.
    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

    Associated conditions

    Description Tests
    Basilicata-Akhtar syndrome
    MedGen: C5231394 OMIM: 301032 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-08-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-08-23)

    ClinGen Genome Curation PagePubMed

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp586J1822

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone reader activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MSL complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MSL complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of NuA4 histone acetyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    MSL complex subunit 3
    Names
    MSL3-like 1
    male-specific lethal 3 homolog
    male-specific lethal-3 protein-like 1

    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_012564.1 RefSeqGene

      Range
      5079..22614
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193270.2 → NP_001180199.1  MSL complex subunit 3 isoform e

      See identical proteins and their annotated locations for NP_001180199.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses a distinct start codon, compared to variant 1. The resulting isoform (e) has a distinct N-terminus and is 12 aa shorter than isoform a.
      Source sequence(s)
      AK300814, BC031210, DA172776, DC395802
      Consensus CDS
      CCDS55369.1
      UniProtKB/TrEMBL
      A0A3B3IT59
      Related
      ENSP00000381538.2, ENST00000398527.7
      Conserved Domains (3) summary
      smart00298
      Location:24 → 66
      CHROMO; Chromatin organization modifier domain
      pfam05712
      Location:145 → 494
      MRG; MRG
      pfam12258
      Location:297 → 401
      Microcephalin; Microcephalin protein

    2. NM_001282174.1 → NP_001269103.1  MSL complex subunit 3 isoform f

      See identical proteins and their annotated locations for NP_001269103.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in its 5' UTR and 5' coding region, and uses a distinct start codon, compared to variant 1. The resulting isoform (f) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AF117065, AK294255, AL713667
      Consensus CDS
      CCDS65213.1
      UniProtKB/TrEMBL
      A0A3F2YNX2
      Related
      ENSP00000354562.2, ENST00000361672.6
      Conserved Domains (2) summary
      pfam05712
      Location:4 → 357
      MRG; MRG
      pfam12258
      Location:160 → 264
      Microcephalin; Microcephalin protein

    3. NM_006800.4 → NP_006791.2  MSL complex subunit 3 isoform c

      See identical proteins and their annotated locations for NP_006791.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The resulting isoform (c) is 166 aa shorter shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC004554, AK025642, CT002798, DA961602
      Consensus CDS
      CCDS14149.1
      UniProtKB/TrEMBL
      A0A3F2YNX2
      Related
      ENSP00000498017.1, ENST00000649078.1
      Conserved Domains (2) summary
      pfam05712
      Location:6 → 340
      MRG
      pfam12258
      Location:143 → 247
      Microcephalin; Microcephalin protein

    4. NM_078628.2 → NP_523352.1  MSL complex subunit 3 isoform d

      See identical proteins and their annotated locations for NP_523352.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (d) has a distinct C-terminus and is 105 aa shorter than isoform a.
      Source sequence(s)
      AF117065, AK000793, AK289780, DB240082
      Consensus CDS
      CCDS14148.1
      UniProtKB/TrEMBL
      A0A3B3ITF3
      Related
      ENSP00000338078.2, ENST00000337339.7
      Conserved Domains (3) summary
      pfam05712
      Location:157 → 289
      MRG; MRG
      pfam11717
      Location:14 → 73
      Tudor-knot; RNA binding activity-knot of a chromodomain
      pfam12258
      Location:309 → 392
      Microcephalin; Microcephalin protein

    5. NM_078629.4 → NP_523353.2  MSL complex subunit 3 isoform a

      See identical proteins and their annotated locations for NP_523353.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC004554, AF117065, BC031210
      Consensus CDS
      CCDS14147.1
      UniProtKB/Swiss-Prot
      A6NCU2, A6NHW8, A8K165, B4DUV8, B7Z227, Q8N5Y2, Q9UG70, Q9Y5Z8
      UniProtKB/TrEMBL
      A0A3B3IT59
      Related
      ENSP00000312244.4, ENST00000312196.10
      Conserved Domains (2) summary
      cd18983
      Location:15 → 81
      CBD_MSL3_like; chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins
      pfam05712
      Location:156 → 506
      MRG

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      11758159..11775772
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      11340708..11358321
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_078630.1: Suppressed sequence

      Description
      NM_078630.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N5Y2.1 GenPept UniProtKB/Swiss-Prot:Q8N5Y2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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