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

Gene ID: 6419, updated on 4-Jan-2025

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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding PubMed 
enables DNA binding PubMed 
enables DNA topoisomerase binding  
enables DNA topoisomerase binding PubMed 
enables double-stranded DNA binding  
enables double-stranded DNA binding PubMed 
enables endonuclease activity PubMed 
enables endonuclease activity PubMed 
enables histone H3K36 dimethyltransferase activity PubMed 
enables histone H3K36 methyltransferase activity  
enables histone H3K36 methyltransferase activity PubMed 
enables histone H3K4 methyltransferase activity  
enables histone H3K4 methyltransferase activity PubMed 
enables protein binding PubMed 
enables protein homodimerization activity PubMed 
enables single-stranded DNA binding  
enables single-stranded DNA binding PubMed 
enables single-stranded DNA endodeoxyribonuclease activity  
enables single-stranded DNA endodeoxyribonuclease activity PubMed 
enables single-stranded DNA endodeoxyribonuclease activity PubMed 
enables zinc ion binding  
Process Evidence Code Pubs
involved_in DNA catabolic process PubMed 
involved_in DNA catabolic process PubMed 
involved_in DNA double-strand break processing  
involved_in DNA double-strand break processing PubMed 
involved_in DNA integration  
involved_in DNA integration PubMed 
involved_in cell population proliferation PubMed 
involved_in chromatin remodeling  
involved_in double-strand break repair via nonhomologous end joining  
involved_in double-strand break repair via nonhomologous end joining PubMed 
involved_in double-strand break repair via nonhomologous end joining PubMed 
involved_in methylation  
involved_in mitotic DNA integrity checkpoint signaling  
involved_in mitotic DNA integrity checkpoint signaling PubMed 
involved_in negative regulation of chromosome organization PubMed 
involved_in nucleic acid metabolic process PubMed 
involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity PubMed 
involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity PubMed 
involved_in positive regulation of double-strand break repair via nonhomologous end joining PubMed 
involved_in replication fork processing  
involved_in replication fork processing PubMed 
Component Evidence Code Pubs
colocalizes_with condensed chromosome  
colocalizes_with condensed chromosome PubMed 
located_in nucleolus  
is_active_in nucleus  
located_in nucleus PubMed 
located_in nucleus PubMed 
is_active_in site of double-strand break  
located_in site of double-strand break PubMed 
located_in site of double-strand break 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)

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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_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

    UniProtKB/TrEMBL
    Q96H41
  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

    UniProtKB/TrEMBL
    Q96H41
  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

    UniProtKB/TrEMBL
    Q96H41

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