setdb1b SET domain bifurcated histone lysine methyltransferase 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: setdb1bprovided by ZNC
Official Full Name: SET domain bifurcated histone lysine methyltransferase 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-061013-224
See related: Ensembl:ENSDARG00000099021 AllianceGenome:ZFIN:ZDB-GENE-061013-224
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: im:7143091; wu:fa04a12; wu:fj80h02; zgc:152899
Summary: Predicted to enable histone H3K9 methyltransferase activity and promoter-specific chromatin binding activity. Predicted to be involved in heterochromatin organization; negative regulation of gene expression; and positive regulation of DNA methylation-dependent heterochromatin formation. Predicted to act upstream of or within chromatin organization and methylation. Predicted to be located in chromosome. 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, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 16

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (21891805..21917328, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (22087553..22113104, complement)

Chromosome 16 - NC_007127.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Atf7ip and Setdb1 interaction orchestrates the hematopoietic stem and progenitor cell state with diverse lineage differentiation.
Title: Atf7ip and Setdb1 interaction orchestrates the hematopoietic stem and progenitor cell state with diverse lineage differentiation.

Submit: New GeneRIF Correction

General gene information

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Markers

fj80h02.x1 (e-PCR)
- UniSTS:199972

fa04a12.s1 (e-PCR)
- UniSTS:202184

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein-lysine N-methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within methylation	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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETDB1-B

Names: SET domain, bifurcated 1b

NP_001070745.3

EC 2.1.1.354

XP_005158070.2

EC 2.1.1.354

XP_005158072.2

EC 2.1.1.354

XP_005158073.2

EC 2.1.1.354

XP_068070115.1

EC 2.1.1.354

XP_068070116.1

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_001077277.3 → NP_001070745.3 histone-lysine N-methyltransferase SETDB1-B

See identical proteins and their annotated locations for NP_001070745.3

Status: VALIDATED

Source sequence(s)

FP929011

UniProtKB/Swiss-Prot

Q06ZW4, Q08BR4

UniProtKB/TrEMBL

A0A0R4IPA3, A0A8M1NBP0

Related

ENSDARP00000136505.1, ENSDART00000165824.2

Conserved Domains (5) summary

smart00333
Location:367 → 418

TUDOR; Tudor domain

smart00317
Location:1114 → 1191

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

cd01395
Location:610 → 671

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 ...

pfam05033
Location:693 → 806

Pre-SET; Pre-SET motif

cl02573
Location:277 → 336

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007127.7 Reference GRCz11 Primary Assembly

Range

21891805..21917328 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158015.5 → XP_005158072.2 histone-lysine N-methyltransferase SETDB1-B isoform X2

UniProtKB/Swiss-Prot

Q06ZW4, Q08BR4

UniProtKB/TrEMBL

A0A8M2B4Z0

Conserved Domains (5) summary

smart00333
Location:395 → 446

TUDOR; Tudor domain

smart00317
Location:1126 → 1203

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

cd01395
Location:638 → 699

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 ...

pfam05033
Location:721 → 834

Pre-SET; Pre-SET motif

cl02573
Location:305 → 364

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
XM_005158013.5 → XP_005158070.2 histone-lysine N-methyltransferase SETDB1-B isoform X1

UniProtKB/Swiss-Prot

Q06ZW4, Q08BR4

UniProtKB/TrEMBL

A0A0R4IUW4, A0A8M2B4C2

Related

ENSDARP00000140273.2, ENSDART00000170634.2

Conserved Domains (5) summary

smart00333
Location:395 → 446

TUDOR; Tudor domain

smart00317
Location:1142 → 1219

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

cd01395
Location:638 → 699

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 ...

pfam05033
Location:721 → 834

Pre-SET; Pre-SET motif

cl02573
Location:305 → 364

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
XM_068214015.1 → XP_068070116.1 histone-lysine N-methyltransferase SETDB1-B isoform X4
XM_068214014.1 → XP_068070115.1 histone-lysine N-methyltransferase SETDB1-B isoform X4
XM_005158016.5 → XP_005158073.2 histone-lysine N-methyltransferase SETDB1-B isoform X3

See identical proteins and their annotated locations for XP_005158073.2

UniProtKB/Swiss-Prot

Q06ZW4, Q08BR4

UniProtKB/TrEMBL

A0A0R4IPA3, A0A8M1NBP0

Conserved Domains (5) summary

smart00333
Location:367 → 418

TUDOR; Tudor domain

smart00317
Location:1114 → 1191

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

cd01395
Location:610 → 671

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 ...

pfam05033
Location:693 → 806

Pre-SET; Pre-SET motif

cl02573
Location:277 → 336

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...