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

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

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_001243723.2NP_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:363442
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:246308
      HTH_32; Homeodomain-like domain
      cl02566
      Location:139163
      SET; SET domain
      cl02622
      Location:27123
      Pre-SET; Pre-SET motif
    2. NM_001276325.2NP_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:139268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cl02622
      Location:27123
      Pre-SET; Pre-SET motif
    3. NM_001320676.2NP_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:224303
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:107169
      HTH_32; Homeodomain-like domain
    4. NM_001320677.2NP_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:246325
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:129191
      HTH_32; Homeodomain-like domain
    5. NM_001320678.2NP_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:214293
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:97159
      HTH_32; Homeodomain-like domain
    6. NM_006515.4NP_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:139268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam01359
      Location:502581
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:385447
      HTH_32; Homeodomain-like domain
      cl02622
      Location:27123
      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_047448716.1XP_047304672.1  histone-lysine N-methyltransferase SETMAR isoform X4

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

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

    4. XM_006713292.4XP_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:266345
      Transposase_1; Transposase (partial DDE domain)
      pfam13565
      Location:149211
      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_054347537.1XP_054203512.1  histone-lysine N-methyltransferase SETMAR isoform X4

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

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

    4. XM_054347534.1XP_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.