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

Summary

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

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_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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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

EC 2.1.1.357

XP_006237058.1

EC 2.1.1.357

XP_006237059.1

EC 2.1.1.357

XP_038964125.2

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_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

NC_086022.1 Reference GRCr8

Range

142602066..142614208

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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