Setd1a SET domain containing 1A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setd1aprovided by MGI
Official Full Name: SET domain containing 1Aprovided by MGI
Primary source: MGI:MGI:2446244
See related: Ensembl:ENSMUSG00000042308 AllianceGenome:MGI:2446244
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: KMT2F; mNSC1; Nsccn1; mKIAA0339
Summary: Enables histone H3K4 methyltransferase activity. Involved in several processes, including positive regulation of gene expression; regulation of chromatin organization; and regulation of erythrocyte differentiation. Acts upstream of or within positive regulation of neural precursor cell proliferation; positive regulation of stem cell proliferation; and stem cell population maintenance. Located in euchromatin and nucleus. Is expressed in several structures, including early conceptus; integumental system; liver; nervous system; and oocyte. Used to study schizophrenia. Human ortholog(s) of this gene implicated in early-onset epilepsy 2 and neurodevelopmental disorder with speech impairment and dysmorphic facies. Orthologous to human SETD1A (SET domain containing 1A, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in limb E14.5 (RPKM 7.1), thymus adult (RPKM 7.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 F3; 7 69.73 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (127376561..127399294)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (127777389..127800122)

Chromosome 7 - NC_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sex-dependent effects of Setd1a haploinsufficiency on development and adult behaviour.
Title: Sex-dependent effects of Setd1a haploinsufficiency on development and adult behaviour.
Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a.
Title: Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a.
Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function.
Title: Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function.
Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.
Title: Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.
Setd1a Plays Pivotal Roles for the Survival and Proliferation of Retinal Progenitors via Histone Modifications of Uhrf1.
Title: Setd1a Plays Pivotal Roles for the Survival and Proliferation of Retinal Progenitors via Histone Modifications of Uhrf1.
Setd1a Insufficiency in Mice Attenuates Excitatory Synaptic Function and Recapitulates Schizophrenia-Related Behavioral Abnormalities.
Title: Setd1a Insufficiency in Mice Attenuates Excitatory Synaptic Function and Recapitulates Schizophrenia-Related Behavioral Abnormalities.
Mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics accompanied by working memory deficits. Setd1a binds both promoters and enhancers with a striking overlap between Setd1a and Mef2 on enhancers. Reinstating Setd1a expression in adulthood rescues cognitive deficits.
Title: Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice.
SET1A-mediated mono-methylation at K342 is an essential regulatory mechanism for regulating YAP activity and tumorigenesis.
Title: SET1A-Mediated Mono-Methylation at K342 Regulates YAP Activation by Blocking Its Nuclear Export and Promotes Tumorigenesis.
The comprehensive regulation of DNA damage responses by SETD1A in HSCs is clearly distinct from the key roles played by other epigenetic regulators, including the major leukemogenic H3K4 methyltransferase MLL1, or MLL5, indicating that HSC identity and function is supported by cooperative specificities within an epigenetic framework.
Title: SETD1A protects HSCs from activation-induced functional decline in vivo.
Study report that Uhrf1 forms a complex with the active trithorax group, the Setd1a/COMPASS complex, to maintain bivalent histone marks, particularly those associated with neuroectoderm and mesoderm specification.
Title: Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU015105 (e-PCR)
- UniSTS:208205

BB098564 (e-PCR)
- UniSTS:185733

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables histone H3K4 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4 methyltransferase activity	ISO Inferred from Sequence Orthology more info
contributes_to histone H3K4 methyltransferase activity	NAS Non-traceable Author Statement more info	PubMed
contributes_to histone H3K4 methyltransferase activity	TAS Traceable Author Statement more info	PubMed
enables histone H3K4 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of chromatin organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of chromatin organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of hematopoietic stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription initiation-coupled chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of Set1C/COMPASS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Set1C/COMPASS complex	ISO Inferred from Sequence Orthology more info
part_of Set1C/COMPASS complex	TAS Traceable Author Statement more info	PubMed
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
part_of histone methyltransferase complex	ISO Inferred from Sequence Orthology more info	PubMed
part_of histone methyltransferase complex	TAS Traceable Author Statement more info	PubMed
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD1A

Names: SET domain-containing protein 1A; non-selective cation channel 1

NP_821172.2

EC 2.1.1.364

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_178029.3 → NP_821172.2 histone-lysine N-methyltransferase SETD1A

Status: VALIDATED

Source sequence(s)

AC149222

Consensus CDS

CCDS40144.1

UniProtKB/Swiss-Prot

E9PYH6

Related

ENSMUSP00000037600.7, ENSMUST00000047157.13

Conserved Domains (5) summary

smart00317
Location:1577 → 1700

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

smart00508
Location:1700 → 1716

PostSET; Cysteine-rich motif following a subset of SET domains

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1434 → 1571

N-SET; COMPASS (Complex proteins associated with Set1p) component N

cl02774
Location:835 → 883

Topoisomer_IB_N; Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA ...

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_000073.7 Reference GRCm39 C57BL/6J

Range

127376561..127399294

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_010940.1: Suppressed sequence

Description

NM_010940.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.