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

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: mouse all
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Genomic context

Location:: 3p26.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (4303369..4317265)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (4297118..4311014)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (4345053..4358949)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

EC 2.1.1.357

NP_001263254.1

EC 2.1.1.357

NP_001307605.1

EC 2.1.1.357

NP_001307606.1

EC 2.1.1.357

NP_001307607.1

EC 2.1.1.357

NP_006506.3

EC 2.1.1.357

XP_006713355.1

EC 2.1.1.357

XP_047304670.1

EC 2.1.1.357

XP_047304671.1

EC 2.1.1.357

XP_047304672.1

EC 2.1.1.357

XP_054203509.1

EC 2.1.1.357

XP_054203510.1

EC 2.1.1.357

XP_054203511.1

EC 2.1.1.357

XP_054203512.1

EC 2.1.1.357

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)

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
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
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
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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

4303369..4317265

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047448716.1 → XP_047304672.1 histone-lysine N-methyltransferase SETMAR isoform X4
XM_047448714.1 → XP_047304670.1 histone-lysine N-methyltransferase SETMAR isoform X2
XM_047448715.1 → XP_047304671.1 histone-lysine N-methyltransferase SETMAR isoform X3
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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

4297118..4311014

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347537.1 → XP_054203512.1 histone-lysine N-methyltransferase SETMAR isoform X4
XM_054347535.1 → XP_054203510.1 histone-lysine N-methyltransferase SETMAR isoform X2
XM_054347536.1 → XP_054203511.1 histone-lysine N-methyltransferase SETMAR isoform X3
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

NR_024022.1: Suppressed sequence

Description

NR_024022.1: This RefSeq was removed because currently there is insufficient support for the transcript.