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    Setmar SET domain and mariner transposase fusion gene [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500281, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Setmarprovided by RGD
    Official Full Name
    SET domain and mariner transposase fusion geneprovided by RGD
    Primary source
    RGD:1565882
    See related
    EnsemblRapid:ENSRNOG00000006806 AllianceGenome:RGD:1565882
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    This gene encodes a histone-lysine N-methyltransferase that may be involved in the methylation of histone H3. In anthropoid primates this gene is a fusion gene of a SET histone-lysine N-methyltransferase and a mariner (MAR) family transposase. In all other species this gene contains only the SET domain. [provided by RefSeq, Feb 2013]
    Expression
    Biased expression in Adrenal (RPKM 24.6), Kidney (RPKM 24.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Setmar in Genome Data Viewer
    Location:
    4q41
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (142602066..142614208)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (141046058..141058183)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (140092346..140104495)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene actin, gamma 1, pseudogene 3 Neighboring gene uncharacterized LOC134486830 Neighboring gene uncharacterized LOC134486831 Neighboring gene sulfatase modifying factor 1 Neighboring gene inositol 1,4,5-trisphosphate receptor, type 1 Neighboring gene uncharacterized LOC102547466

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The DDN catalytic motif is required for Metnase functions in non-homologous end joining (NHEJ) repair and replication restart. Kim HS, et al. J Biol Chem, 2014 Apr 11. PMID 24573677, Free PMC Article
    2. Biochemical characterization of metnase's endonuclease activity and its role in NHEJ repair. Beck BD, et al. Biochemistry, 2011 May 24. PMID 21491884, Free PMC Article
    3. Crystal structure of the human Hsmar1-derived transposase domain in the DNA repair enzyme Metnase. Goodwin KD, et al. Biochemistry, 2010 Jul 13. PMID 20521842
    4. The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair. Lee SH, et al. Proc Natl Acad Sci U S A, 2005 Dec 13. PMID 16332963, Free PMC Article
    5. Chk1 phosphorylation of Metnase enhances DNA repair but inhibits replication fork restart. Hromas R, et al. Oncogene, 2012 Sep 20. PMID 22231448, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA topoisomerase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 dimethyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 dimethyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3K36 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3K9 methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA endodeoxyribonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA double-strand break processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA integration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic DNA integrity checkpoint signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of chromosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in replication fork processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in condensed chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETMAR
    Names
    SET domain and mariner transposase fusion gene-containing protein homolog
    SET domain and mariner transposase fusion protein homolog
    SET domain without mariner transposase fusion
    NP_001020219.1
    XP_006237058.1
    XP_006237059.1
    XP_038964125.2

    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_001025048.1 → NP_001020219.1  histone-lysine N-methyltransferase SETMAR

      See identical proteins and their annotated locations for NP_001020219.1

      Status: PROVISIONAL

      Source sequence(s)
      BC088181
      UniProtKB/Swiss-Prot
      Q5I0M0
      UniProtKB/TrEMBL
      A6IBK7, G3V6U2
      Related
      ENSRNOP00000008892.5, ENSRNOT00000008892.8
      Conserved Domains (2) summary
      smart00317
      Location:142 → 269
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam05033
      Location:29 → 132
      Pre-SET; Pre-SET motif

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      142602066..142614208
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006236996.5 → XP_006237058.1  histone-lysine N-methyltransferase SETMAR isoform X1

      UniProtKB/TrEMBL
      A6IBK7, G3V6U2
      Conserved Domains (2) summary
      smart00317
      Location:96 → 223
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam05033
      Location:7 → 86
      Pre-SET; Pre-SET motif

    2. XM_039108197.2 → XP_038964125.2  histone-lysine N-methyltransferase SETMAR isoform X2

    3. XM_006236997.5 → XP_006237059.1  histone-lysine N-methyltransferase SETMAR isoform X3

      See identical proteins and their annotated locations for XP_006237059.1

      UniProtKB/TrEMBL
      A0A8I5ZK94, A6IBK7, A6IBK8, G3V6U2
      Conserved Domains (2) summary
      smart00317
      Location:111 → 238
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam05033
      Location:22 → 101
      Pre-SET; Pre-SET motif
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5I0M0.1 GenPept UniProtKB/Swiss-Prot:Q5I0M0

    Gene LinkOut

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

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