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

Gene ID: 6419, updated on 8-Dec-2018

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
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

Genomic context

See SETMAR in Genome Data Viewer
Location:
3p26.1
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (4303304..4320649)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (4344988..4358949)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723512 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1 Neighboring gene sulfatase modifying factor 1 Neighboring gene uncharacterized LOC107986008 Neighboring gene mitochondrial ribosomal protein S10 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA topoisomerase binding IPI
Inferred from Physical Interaction
more info
PubMed 
double-stranded DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
endonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
endonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone methyltransferase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
single-stranded DNA endodeoxyribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA catabolic process, endonucleolytic IDA
Inferred from Direct Assay
more info
PubMed 
DNA catabolic process, endonucleolytic IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA double-strand break processing IDA
Inferred from Direct Assay
more info
PubMed 
DNA integration IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-strand break repair via nonhomologous end joining IDA
Inferred from Direct Assay
more info
PubMed 
double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3-K36 dimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3-K36 methylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3-K4 methylation IDA
Inferred from Direct Assay
more info
PubMed 
mitotic DNA integrity checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell cycle arrest IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of chromosome organization IDA
Inferred from Direct Assay
more info
PubMed 
nucleic acid phosphodiester bond hydrolysis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of double-strand break repair via nonhomologous end joining IDA
Inferred from Direct Assay
more info
PubMed 
replication fork processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IC
Inferred by Curator
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
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_006713357.1

NCBI Reference Sequences (RefSeq)

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_001243723.1NP_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, AK222734, AK302296, DC357038
    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_001276325.1NP_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)
    AK307537, BC011635
    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_001320676.1NP_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)
    AK307537, BC008931
    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_001320677.1NP_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)
    AK222734, AK297865, AK307537
    UniProtKB/Swiss-Prot
    Q53H47
    UniProtKB/TrEMBL
    B4DND2
    Conserved Domains (2) summary
    pfam01359
    Location:246325
    Transposase_1; Transposase (partial DDE domain)
    pfam13565
    Location:129191
    HTH_32; Homeodomain-like domain
  5. NM_001320678.1NP_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)
    AK222734, AK307537
    UniProtKB/Swiss-Prot
    Q53H47
    Conserved Domains (2) summary
    pfam01359
    Location:214293
    Transposase_1; Transposase (partial DDE domain)
    pfam13565
    Location:97159
    HTH_32; Homeodomain-like domain
  6. NM_006515.3NP_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)
    AK222734, DC357038
    Consensus CDS
    CCDS2563.2
    UniProtKB/Swiss-Prot
    Q53H47
    Related
    ENSP00000373354.3, ENST00000358065.4
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    4303304..4320649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713292.3XP_006713355.1  histone-lysine N-methyltransferase SETMAR isoform X1

    See identical proteins and their annotated locations for XP_006713355.1

    Conserved Domains (2) summary
    pfam01359
    Location:266345
    Transposase_1; Transposase (partial DDE domain)
    pfam13565
    Location:149211
    HTH_32; Homeodomain-like domain
  2. XM_006713294.4XP_006713357.1  histone-lysine N-methyltransferase SETMAR isoform X2

    See identical proteins and their annotated locations for XP_006713357.1

    UniProtKB/TrEMBL
    B4DND2
    Conserved Domains (2) summary
    pfam01359
    Location:246325
    Transposase_1; Transposase (partial DDE domain)
    pfam13565
    Location:129191
    HTH_32; Homeodomain-like domain

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.
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