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    SETMAR SET domain and mariner transposase fusion gene [ Homo sapiens (human) ]

    Gene ID: 6419, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SETMARprovided by HGNC
    Official Full Name
    SET domain and mariner transposase fusion geneprovided by HGNC
    Primary source
    HGNC:HGNC:10762
    See related
    Ensembl:ENSG00000170364 MIM:609834; AllianceGenome:HGNC:10762
    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
    Mar1; METNASE
    Summary
    This gene encodes a fusion protein that contains an N-terminal histone-lysine N-methyltransferase domain and a C-terminal mariner transposase domain. The encoded protein binds DNA and functions in DNA repair activities including non-homologous end joining and double strand break repair. The SET domain portion of this protein specifically methylates histone H3 lysines 4 and 36. This gene exists as a fusion gene only in anthropoid primates, other organisms lack mariner transposase domain. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
    Expression
    Ubiquitous expression in ovary (RPKM 4.0), endometrium (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETMAR in Genome Data Viewer
    Location:
    3p26.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (4303369..4317265)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4297118..4311014)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (4345053..4358949)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723512 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4107004-4107504 Neighboring gene sulfatase modifying factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:4344650-4345392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19346 Neighboring gene Sharpr-MPRA regulatory region 4455 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4417841-4418341 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4417340-4417840 Neighboring gene Sharpr-MPRA regulatory region 6601 Neighboring gene Sharpr-MPRA regulatory region 14120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19347 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:4473683-4474469 Neighboring gene mitochondrial ribosomal protein S10 pseudogene 2 Neighboring gene uncharacterized LOC124909340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19348

    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. Fidelity of end joining in mammalian episomes and the impact of Metnase on joint processing. Rath A, et al. BMC Mol Biol, 2014 Mar 22. PMID 24655462, Free PMC Article
    2. Potential role for the Metnase transposase fusion gene in colon cancer through the regulation of key genes. Apostolou P, et al. PLoS One, 2014. PMID 25333365, Free PMC Article
    3. The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Miskey C, et al. Mol Cell Biol, 2007 Jun. PMID 17403897, Free PMC Article
    4. The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. Liu D, et al. Mol Cell Biol, 2007 Feb. PMID 17130240, Free PMC Article
    5. The SET Domain Is Essential for Metnase Functions in Replication Restart and the 5' End of SS-Overhang Cleavage. Kim HS, et al. PLoS One, 2015. PMID 26437079, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Investigating the Expression Pattern of the SETMAR Gene Transcript Variants in Childhood Acute Leukemia: Revisiting an Old Gene.
      Title: Investigating the Expression Pattern of the SETMAR Gene Transcript Variants in Childhood Acute Leukemia: Revisiting an Old Gene.
    2. Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing.
      Title: Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing.
    3. Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells.
      Title: Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells.
    4. Mutation and expression alterations of histone methylation-related NSD2, KDM2B and SETMAR genes in colon cancers.
      Title: Mutation and expression alterations of histone methylation-related NSD2, KDM2B and SETMAR genes in colon cancers.
    5. The roles of the human SETMAR protein in illegitimate DNA recombination and non-homologous end joining repair were studied. Contrary to previous reports, it was found that wild type SETMAR had little to no effect on the rate of cell division, DNA integration into the genome or non-homologous end joining.
      Title: The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair.
    6. ur data is consistent with a model in which SETMAR is part of an anthropoid primate-specific regulatory network centered on the subset of genes containing a transposon end.
      Title: Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome.
    7. Various SETMAR proteins can be synthesized in human glioblastoma that may each have specific biophysical and/or biochemical properties and characteristics.
      Title: SETMAR isoforms in glioblastoma: A matter of protein stability.
    8. These results suggest that Metnase enhances Exo1-mediated exonuclease activity on the lagging strand DNA by facilitating Exo1 loading onto a single strand gap at the stalled replication fork.
      Title: Metnase Mediates Loading of Exonuclease 1 onto Single Strand Overhang DNA for End Resection at Stalled Replication Forks.
    9. The SET domain is needed for the 5' end of ss-overhang cleavage with fork and non-fork DNA without affecting the Metnase-DNA interaction. This domain has a positive role in restart of replication fork and the 5' end of ss-overhang cleavage.
      Title: The SET Domain Is Essential for Metnase Functions in Replication Restart and the 5' End of SS-Overhang Cleavage.
    10. methylation of snRNP70 by SETMAR regulates constitutive and/or alternative splicing
      Title: A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of chronic periodontitis in a general German population.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA topoisomerase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA topoisomerase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables endonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K36 dimethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K36 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables single-stranded DNA endodeoxyribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA endodeoxyribonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded DNA endodeoxyribonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA double-strand break processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA double-strand break processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA integration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA integration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic DNA integrity checkpoint signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic DNA integrity checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of chromosome organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nucleic acid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in replication fork processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in replication fork processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with condensed chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with condensed chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of double-strand break IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETMAR
    Names
    SET domain and mariner transposase fusion gene-containing protein
    SET domain and mariner transposase fusion protein
    NP_001230652.1
    NP_001263254.1
    NP_001307605.1
    NP_001307606.1
    NP_001307607.1
    NP_006506.3
    XP_006713355.1
    XP_047304670.1
    XP_047304671.1
    XP_047304672.1
    XP_054203509.1
    XP_054203510.1
    XP_054203511.1
    XP_054203512.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001243723.2 → NP_001230652.1  histone-lysine N-methyltransferase SETMAR isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC023483, AC034191
      Consensus CDS
      CCDS58814.1
      UniProtKB/Swiss-Prot
      Q53H47
      Related
      ENSP00000403145.1, ENST00000425863.5
      Conserved Domains (4) summary
      pfam01359
      Location:363 → 442
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:246 → 308
      HTH_32; Homeodomain-like domain
      cl02566
      Location:139 → 163
      SET; SET domain
      cl02622
      Location:27 → 123
      Pre-SET; Pre-SET motif

    2. NM_001276325.2 → NP_001263254.1  histone-lysine N-methyltransferase SETMAR isoform 3

      See identical proteins and their annotated locations for NP_001263254.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks the terminal exon and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1. This isoform 3 lacks the mariner transposase domain found in isoform 1.
      Source sequence(s)
      AC023483, AC034191
      Consensus CDS
      CCDS63528.1
      UniProtKB/Swiss-Prot
      Q53H47
      Related
      ENSP00000403000.1, ENST00000430981.1
      Conserved Domains (2) summary
      smart00317
      Location:139 → 268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl02622
      Location:27 → 123
      Pre-SET; Pre-SET motif

    3. NM_001320676.2 → NP_001307605.1  histone-lysine N-methyltransferase SETMAR isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in its 5' coding region, which results in the use of an alternate start codon and a frameshift, compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC023483, AC034191
      UniProtKB/TrEMBL
      Q96H41
      Conserved Domains (2) summary
      pfam01359
      Location:224 → 303
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:107 → 169
      HTH_32; Homeodomain-like domain

    4. NM_001320677.2 → NP_001307606.1  histone-lysine N-methyltransferase SETMAR isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses alternate splice sites in its 5' coding region, which results in the use of an alternate start codon and a frameshift, compared to variant 1. The encoded isoform (6) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC023483, AC034191
      UniProtKB/TrEMBL
      B4DND2, Q96H41
      Conserved Domains (2) summary
      pfam01359
      Location:246 → 325
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:129 → 191
      HTH_32; Homeodomain-like domain

    5. NM_001320678.2 → NP_001307607.1  histone-lysine N-methyltransferase SETMAR isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (7) is shorter than isoform 1.
      Source sequence(s)
      AC023483, AC034191
      UniProtKB/TrEMBL
      Q96H41
      Conserved Domains (2) summary
      pfam01359
      Location:214 → 293
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:97 → 159
      HTH_32; Homeodomain-like domain

    6. NM_006515.4 → NP_006506.3  histone-lysine N-methyltransferase SETMAR isoform 1

      See identical proteins and their annotated locations for NP_006506.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC023483, AC034191
      Consensus CDS
      CCDS2563.2
      UniProtKB/Swiss-Prot
      B4DY74, E7EN68, Q13579, Q1G668, Q53H47, Q96F41
      Related
      ENSP00000373354.3, ENST00000358065.5
      Conserved Domains (4) summary
      smart00317
      Location:139 → 268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam01359
      Location:502 → 581
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:385 → 447
      HTH_32; Homeodomain-like domain
      cl02622
      Location:27 → 123
      Pre-SET; Pre-SET motif

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      4303369..4317265
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448716.1 → XP_047304672.1  histone-lysine N-methyltransferase SETMAR isoform X4

    2. XM_047448714.1 → XP_047304670.1  histone-lysine N-methyltransferase SETMAR isoform X2

    3. XM_047448715.1 → XP_047304671.1  histone-lysine N-methyltransferase SETMAR isoform X3

    4. XM_006713292.4 → XP_006713355.1  histone-lysine N-methyltransferase SETMAR isoform X1

      See identical proteins and their annotated locations for XP_006713355.1

      UniProtKB/TrEMBL
      Q96H41
      Conserved Domains (2) summary
      pfam01359
      Location:266 → 345
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:149 → 211
      HTH_32; Homeodomain-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      4297118..4311014
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347537.1 → XP_054203512.1  histone-lysine N-methyltransferase SETMAR isoform X4

    2. XM_054347535.1 → XP_054203510.1  histone-lysine N-methyltransferase SETMAR isoform X2

    3. XM_054347536.1 → XP_054203511.1  histone-lysine N-methyltransferase SETMAR isoform X3

    4. XM_054347534.1 → XP_054203509.1  histone-lysine N-methyltransferase SETMAR isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_024022.1: Suppressed sequence

      Description
      NR_024022.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q53H47.2 GenPept UniProtKB/Swiss-Prot:Q53H47

    Gene LinkOut

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

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