Setd5 SET domain containing 5 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setd5provided by MGI
Official Full Name: SET domain containing 5provided by MGI
Primary source: MGI:MGI:1920145
See related: Ensembl:ENSMUSG00000034269 AllianceGenome:MGI:1920145
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: mKIAA1757; C330007C20; 2900045N06Rik
Summary: Enables histone H3K36 methyltransferase activity; histone H3K9 methyltransferase activity; and transcription corepressor activity. Involved in several processes, including regulation of DNA-templated transcription; regulation of chromatin organization; and regulation of synapse assembly. Located in euchromatin and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 23. Orthologous to human SETD5 (SET domain containing 5). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in limb E14.5 (RPKM 17.8), CNS E11.5 (RPKM 13.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 E3; 6 52.73 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (113054326..113130393)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (113077262..113153432)

Chromosome 6 - NC_000072.7 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?

Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.
Title: Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.
SETD5 haploinsufficiency affects mitochondrial compartment in neural cells.
Title: SETD5 haploinsufficiency affects mitochondrial compartment in neural cells.
Setd5, but not Setd2, is indispensable for retinal cell survival and proliferation.
Title: Setd5, but not Setd2, is indispensable for retinal cell survival and proliferation.
Setd5 is required in cardiopharyngeal mesoderm for heart development and its haploinsufficiency is associated with outflow tract defects in mouse.
Title: Setd5 is required in cardiopharyngeal mesoderm for heart development and its haploinsufficiency is associated with outflow tract defects in mouse.
Spatiotemporal dynamics of SETD5-containing NCoR-HDAC3 complex determines enhancer activation for adipogenesis.
Title: Spatiotemporal dynamics of SETD5-containing NCoR-HDAC3 complex determines enhancer activation for adipogenesis.
Setd5 haploinsufficiency impairs the proliferative dynamics of neural progenitors and synaptic wiring of neurons, ultimately resulting in behavioral deficits in mice. Setd5 gene loss leads to abnormal transcription, with impaired RNA maturation causing detrimental effects on gene integrity and splicing.
Title: SETD5 Regulates Chromatin Methylation State and Preserves Global Transcriptional Fidelity during Brain Development and Neuronal Wiring.
A specific subpopulation of fetal Setd5(+/-) cortical neurons showed altered gene expression of neurodevelopment-related genes. Setd5(+/-) animals manifested several autism-like behaviors, including hyperactivity, cognitive deficit, and altered social interactions. Anatomical differences were observed in Setd5(+/-) adult brains, accompanied by a deficit of deep-layer cortical neurons in the developing brain.
Title: Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice.
Setd5-haploinsufficient mice present abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Setd5-mutant mice show impairments in cognitive tasks, enhanced LTP, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition.
Title: Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.
Both SetD5 and BRD2 bind to the transcription start site and to upstream promoter regions of the Sema3a locus and BRD2 is necessary for the regulation of Sema3A expression by SetD5.
Title: miR-126-5p promotes retinal endothelial cell survival through SetD5 regulation in neurons.
The findings suggest that SETD5 is essential for regulating histone acetylation during gene transcription and plays a vital role in mammalian embryonic development, and cell cycle progression.
Title: Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G66214 (e-PCR)
- UniSTS:230202

Setd5 (e-PCR), detects polymorphism
- UniSTS:507217

RH127206 (e-PCR)
- UniSTS:208010

RH136591 (e-PCR)
- UniSTS:210571

RH12737 (e-PCR)
- UniSTS:64710

D6Oda20 (e-PCR), detects polymorphism
- UniSTS:515326

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
NOT enables histone H3 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in cognition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase III	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA-templated transcription elongation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Rpd3L-Expanded complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Set3 complex	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD5

Names: SET domain-containing protein 5

NP_082661.1

EC 2.1.1.359

EC 2.1.1.367

NP_766593.1

EC 2.1.1.359

EC 2.1.1.367

XP_006506740.1

EC 2.1.1.359

EC 2.1.1.367

XP_011239782.1

EC 2.1.1.359

EC 2.1.1.367

XP_011239784.1

EC 2.1.1.359

EC 2.1.1.367

XP_011239786.1

EC 2.1.1.359

EC 2.1.1.367

XP_011239787.1

EC 2.1.1.359

EC 2.1.1.367

XP_017177260.1

EC 2.1.1.359

EC 2.1.1.367

XP_017177261.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111467.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111468.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111469.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111470.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111471.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111472.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111473.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111474.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111476.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111477.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111478.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111480.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111481.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111482.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111483.1

EC 2.1.1.359

EC 2.1.1.367

XP_030111484.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008223.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008224.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008225.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008226.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008227.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008228.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008229.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008230.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008231.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008232.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008233.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008234.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008235.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008236.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008237.1

EC 2.1.1.359

EC 2.1.1.367

XP_036008238.1

EC 2.1.1.359

EC 2.1.1.367

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_028385.1 → NP_082661.1 histone-lysine N-methyltransferase SETD5 isoform 1

See identical proteins and their annotated locations for NP_082661.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the shorter isoform (1).

Source sequence(s)

AK122551

Consensus CDS

CCDS20411.1

UniProtKB/Swiss-Prot

Q5XJV7, Q80T94, Q8BKD5, Q8BX30

Related

ENSMUSP00000047398.6, ENSMUST00000042889.12

Conserved Domains (1) summary

smart00317
Location:286 → 395

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
NM_173005.1 → NP_766593.1 histone-lysine N-methyltransferase SETD5 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 2 which has a longer N-terminus compared to isoform 1.

Source sequence(s)

AK053541, BC083184, BE446905, BF456249

Consensus CDS

CCDS90096.1

UniProtKB/Swiss-Prot

Q5XJV7

Related

ENSMUSP00000108780.2, ENSMUST00000113155.2

Conserved Domains (1) summary

cd19181
Location:285 → 434

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

113054326..113130393

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011241485.4 → XP_011239787.1 histone-lysine N-methyltransferase SETD5 isoform X6

See identical proteins and their annotated locations for XP_011239787.1

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_011241480.4 → XP_011239782.1 histone-lysine N-methyltransferase SETD5 isoform X1

See identical proteins and their annotated locations for XP_011239782.1

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_011241482.4 → XP_011239784.1 histone-lysine N-methyltransferase SETD5 isoform X2

UniProtKB/Swiss-Prot

Q5XJV7

Related

ENSMUSP00000108782.2, ENSMUST00000113157.8

Conserved Domains (1) summary

cd19181
Location:285 → 434

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255607.2 → XP_030111467.1 histone-lysine N-methyltransferase SETD5 isoform X3

Conserved Domains (1) summary

cd19181
Location:273 → 422

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255620.2 → XP_030111480.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152332.1 → XP_036008225.1 histone-lysine N-methyltransferase SETD5 isoform X1

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255612.2 → XP_030111472.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152333.1 → XP_036008226.1 histone-lysine N-methyltransferase SETD5 isoform X2

Conserved Domains (1) summary

cd19181
Location:285 → 434

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152331.1 → XP_036008224.1 histone-lysine N-methyltransferase SETD5 isoform X1

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255613.2 → XP_030111473.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152340.1 → XP_036008233.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255614.2 → XP_030111474.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152338.1 → XP_036008231.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152336.1 → XP_036008229.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152330.1 → XP_036008223.1 histone-lysine N-methyltransferase SETD5 isoform X1

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152334.1 → XP_036008227.1 histone-lysine N-methyltransferase SETD5 isoform X3

Conserved Domains (1) summary

cd19181
Location:273 → 422

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152339.1 → XP_036008232.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255622.2 → XP_030111482.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255609.2 → XP_030111469.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_006506677.5 → XP_006506740.1 histone-lysine N-methyltransferase SETD5 isoform X1

See identical proteins and their annotated locations for XP_006506740.1

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255617.2 → XP_030111477.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255621.2 → XP_030111481.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_011241484.4 → XP_011239786.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152341.1 → XP_036008234.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152337.1 → XP_036008230.1 histone-lysine N-methyltransferase SETD5 isoform X5

Conserved Domains (1) summary

cd19181
Location:228 → 377

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_017321772.3 → XP_017177261.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_017321771.3 → XP_017177260.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255616.2 → XP_030111476.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152335.1 → XP_036008228.1 histone-lysine N-methyltransferase SETD5 isoform X3

Conserved Domains (1) summary

cd19181
Location:273 → 422

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255611.2 → XP_030111471.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152343.1 → XP_036008236.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152344.1 → XP_036008237.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255608.2 → XP_030111468.1 histone-lysine N-methyltransferase SETD5 isoform X3

Conserved Domains (1) summary

cd19181
Location:273 → 422

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255610.2 → XP_030111470.1 histone-lysine N-methyltransferase SETD5 isoform X4

Conserved Domains (1) summary

cd19181
Location:247 → 396

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255618.2 → XP_030111478.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255623.2 → XP_030111483.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_030255624.2 → XP_030111484.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152345.1 → XP_036008238.1 histone-lysine N-methyltransferase SETD5 isoform X7

Conserved Domains (1) summary

cd19181
Location:292 → 441

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
XM_036152342.1 → XP_036008235.1 histone-lysine N-methyltransferase SETD5 isoform X6

Conserved Domains (1) summary

cd19181
Location:155 → 304

SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins