Setdb1 SET domain bifurcated histone lysine methyltransferase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Setdb1provided by RGD
Full Name: SET domain bifurcated histone lysine methyltransferase 1provided by RGD
Primary source: RGD:1308370
See related: Ensembl:ENSRNOG00000021143 AllianceGenome:RGD:1308370
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA binding activity; histone methyltransferase activity (H3-K9 specific); and promoter-specific chromatin binding activity. Involved in response to ethanol and response to vitamin. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autistic disorder and lung cancer. Orthologous to human SETDB1 (SET domain bifurcated histone lysine methyltransferase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 213.3), Adrenal (RPKM 212.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (185587722..185619084, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (182898738..182930283, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (196495867..196527412, complement)

Chromosome 2 - NC_086020.1 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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Markers

UniSTS:234764 (e-PCR)
- UniSTS:234764

PMC355869P1 (e-PCR)
- UniSTS:273262

AW535103 (e-PCR)
- UniSTS:247178

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology 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 histone H3K9 trimethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner cell mass cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to vitamin	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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 SETDB1

Names: SET domain, bifurcated 1; histone-lysine N-methyltransferase SETDB1-like

NP_001258104.1

EC 2.1.1.354

XP_006232975.1

EC 2.1.1.354

XP_006232976.1

EC 2.1.1.354

XP_006232979.1

EC 2.1.1.354

XP_038959087.1

EC 2.1.1.354

XP_038959088.1

EC 2.1.1.354

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_001271175.1 → NP_001258104.1 histone-lysine N-methyltransferase SETDB1

See identical proteins and their annotated locations for NP_001258104.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A0A8I6ASK2

Related

ENSRNOP00000073356.2, ENSRNOT00000077325.2

Conserved Domains (5) summary

smart00391
Location:609 → 684

MBD; Methyl-CpG binding domain

smart00333
Location:348 → 400

TUDOR; Tudor domain

smart00317
Location:1217 → 1279

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

pfam05033
Location:694 → 807

Pre-SET; Pre-SET motif

pfam11068
Location:24 → 98

YlqD; YlqD protein

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_086020.1 Reference GRCr8

Range

185587722..185619084 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006232913.4 → XP_006232975.1 histone-lysine N-methyltransferase SETDB1 isoform X1

UniProtKB/TrEMBL

A0A8I6ASK2, D4A081

Related

ENSRNOP00000028709.5

Conserved Domains (5) summary

smart00391
Location:629 → 704

MBD; Methyl-CpG binding domain

smart00333
Location:368 → 420

TUDOR; Tudor domain

smart00317
Location:1237 → 1299

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

pfam05033
Location:714 → 827

Pre-SET; Pre-SET motif

pfam11068
Location:44 → 118

YlqD; YlqD protein
XM_006232914.3 → XP_006232976.1 histone-lysine N-methyltransferase SETDB1 isoform X2

See identical proteins and their annotated locations for XP_006232976.1

UniProtKB/TrEMBL

A0A8I6ASK2

Conserved Domains (5) summary

smart00391
Location:609 → 684

MBD; Methyl-CpG binding domain

smart00333
Location:348 → 400

TUDOR; Tudor domain

smart00317
Location:1217 → 1279

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

pfam05033
Location:694 → 807

Pre-SET; Pre-SET motif

pfam11068
Location:24 → 98

YlqD; YlqD protein
XM_039103159.2 → XP_038959087.1 histone-lysine N-methyltransferase SETDB1 isoform X3

UniProtKB/TrEMBL

A6K2Y7

Conserved Domains (6) summary

smart00391
Location:456 → 531

MBD; Methyl-CpG binding domain

cd10517
Location:533 → 730

SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins

cl40432
Location:1060 → 1149

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

pfam18300
Location:40 → 97

DUF5604; Domain of unknown function (DUF5604)

cd20382
Location:107 → 188

Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins

cd21181
Location:195 → 248

Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
XM_006232917.4 → XP_006232979.1 histone-lysine N-methyltransferase SETDB1 isoform X4

UniProtKB/TrEMBL

A6K2Y7

Conserved Domains (4) summary

smart00391
Location:408 → 483

MBD; Methyl-CpG binding domain

smart00468
Location:490 → 597

PreSET; N-terminal to some SET domains

smart00333
Location:147 → 199

TUDOR; Tudor domain

smart00317
Location:1016 → 1078

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
XM_039103160.2 → XP_038959088.1 histone-lysine N-methyltransferase SETDB1 isoform X5

UniProtKB/TrEMBL

A6K2Y7

Conserved Domains (4) summary

smart00391
Location:265 → 340

MBD; Methyl-CpG binding domain

cd10517
Location:342 → 539

SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins

cl40432
Location:869 → 958

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

cd21181
Location:4 → 57

Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins