Setdb2 SET domain bifurcated histone lysine methyltransferase 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Setdb2provided by RGD
Full Name: SET domain bifurcated histone lysine methyltransferase 2provided by RGD
Primary source: RGD:2319564
See related: EnsemblRapid:ENSRNOG00000021680 AllianceGenome:RGD:2319564
Gene type: protein coding
RefSeq status: MODEL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable histone H3K9 methyltransferase activity. Predicted to be involved in several processes, including chromosome segregation; heterochromatin organization; and regulation of gene expression. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SETDB2 (SET domain bifurcated histone lysine methyltransferase 2). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: 15p12

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (37731029..37782790, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (33553657..33606586, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (38699135..39745035, complement)

Chromosome 15 - NC_086033.1 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D15Rat142 (e-PCR), detects polymorphism
- UniSTS:226702

RH131947 (e-PCR)
- UniSTS:215230

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	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 gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETDB2

Names: PHD finger protein 11; SET domain, bifurcated 2

XP_038949803.1

EC 2.1.1.354

XP_038949804.1

EC 2.1.1.354

XP_038949805.1

EC 2.1.1.354

XP_038949807.1

EC 2.1.1.354

XP_038949808.1

EC 2.1.1.354

XP_038949809.1

EC 2.1.1.354

XP_038949811.1

EC 2.1.1.354

XP_038949812.1

EC 2.1.1.354

XP_038949813.1

EC 2.1.1.354

XP_038949814.1

EC 2.1.1.354

XP_038949815.1

EC 2.1.1.354

XP_038949816.1

EC 2.1.1.354

XP_063130938.1

EC 2.1.1.354

NCBI Reference Sequences (RefSeq)

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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_086033.1 Reference GRCr8

Range

37731029..37782790 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039093876.2 → XP_038949804.1 histone-lysine N-methyltransferase SETDB2 isoform X1

UniProtKB/TrEMBL

A0A8I6GAC4, M0R6H5

Related

ENSRNOP00000084411.1, ENSRNOT00000094078.2

Conserved Domains (4) summary

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cl40432
Location:210 → 687

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam00856
Location:365 → 425

SET; SET domain

cl22851
Location:700 → 813

PHD_SF; PHD finger superfamily
XM_039093875.2 → XP_038949803.1 histone-lysine N-methyltransferase SETDB2 isoform X1

UniProtKB/TrEMBL

A0A8I6GAC4, M0R6H5

Conserved Domains (4) summary

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cl40432
Location:210 → 687

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam00856
Location:365 → 425

SET; SET domain

cl22851
Location:700 → 813

PHD_SF; PHD finger superfamily
XM_039093877.2 → XP_038949805.1 histone-lysine N-methyltransferase SETDB2 isoform X2

Conserved Domains (4) summary

cd01395
Location:100 → 160

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cl40432
Location:158 → 635

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam00856
Location:313 → 373

SET; SET domain

cl22851
Location:648 → 761

PHD_SF; PHD finger superfamily
XM_039093879.2 → XP_038949807.1 histone-lysine N-methyltransferase SETDB2 isoform X3

Conserved Domains (4) summary

cl40432
Location:21 → 498

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam00856
Location:176 → 236

SET; SET domain

cl00110
Location:1 → 23

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

cl22851
Location:511 → 624

PHD_SF; PHD finger superfamily
XM_063274868.1 → XP_063130938.1 histone-lysine N-methyltransferase SETDB2 isoform X4
XM_039093880.2 → XP_038949808.1 histone-lysine N-methyltransferase SETDB2 isoform X4

Conserved Domains (3) summary

cl40432
Location:1 → 346

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam00856
Location:24 → 84

SET; SET domain

cl22851
Location:359 → 472

PHD_SF; PHD finger superfamily
XM_039093885.2 → XP_038949813.1 histone-lysine N-methyltransferase SETDB2 isoform X8

Conserved Domains (2) summary

cl40432
Location:105 → 182

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

cl22851
Location:195 → 308

PHD_SF; PHD finger superfamily
XM_039093883.2 → XP_038949811.1 histone-lysine N-methyltransferase SETDB2 isoform X6

Conserved Domains (3) summary

COG2940
Location:43 → 208

SET; SET domain-containing protein (function unknown) [General function prediction only]

cl40432
Location:145 → 222

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

cl22851
Location:235 → 348

PHD_SF; PHD finger superfamily
XM_039093888.2 → XP_038949816.1 histone-lysine N-methyltransferase SETDB2 isoform X10

Conserved Domains (1) summary

cl22851
Location:27 → 140

PHD_SF; PHD finger superfamily
XM_039093887.2 → XP_038949815.1 histone-lysine N-methyltransferase SETDB2 isoform X10

Conserved Domains (1) summary

cl22851
Location:27 → 140

PHD_SF; PHD finger superfamily
XM_039093886.2 → XP_038949814.1 histone-lysine N-methyltransferase SETDB2 isoform X9

UniProtKB/TrEMBL

F1LQ59

Conserved Domains (1) summary

cl22851
Location:76 → 189

PHD_SF; PHD finger superfamily
XM_039093881.2 → XP_038949809.1 histone-lysine N-methyltransferase SETDB2 isoform X5

UniProtKB/TrEMBL

D3ZDZ9

Related

ENSRNOP00000036240.7, ENSRNOT00000036781.9

Conserved Domains (2) summary

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cl40432
Location:210 → 420

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_039093884.2 → XP_038949812.1 histone-lysine N-methyltransferase SETDB2 isoform X7

Conserved Domains (2) summary

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cl40432
Location:210 → 420

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily