Supt6 SPT6, histone chaperone and transcription elongation factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Supt6provided by MGI
Official Full Name: SPT6, histone chaperone and transcription elongation factorprovided by MGI
Primary source: MGI:MGI:107726
See related: Ensembl:ENSMUSG00000002052 AllianceGenome:MGI:107726
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: SPT6; Supt6h; mKIAA0162; 5131400N11Rik
Summary: Predicted to enable histone binding activity and nucleosome binding activity. Involved in several processes, including negative regulation of histone H3-K27 methylation; regulation of mRNA export from nucleus; and regulation of nucleobase-containing compound metabolic process. Acts upstream of or within blastocyst formation. Predicted to be located in nucleus. Predicted to be part of transcription elongation factor complex. Predicted to be active in transcriptionally active chromatin. Is expressed in several structures, including brain; early conceptus; genitourinary system; liver; and spleen. Orthologous to human SUPT6H (SPT6 homolog, histone chaperone and transcription elongation factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in cerebellum adult (RPKM 12.2), frontal lobe adult (RPKM 11.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B5; 11 46.74 cM

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (78097575..78136798, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (78206749..78245972, complement)

Chromosome 11 - NC_000077.7 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
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?

Iws1 and Spt6 Regulate Trimethylation of Histone H3 on Lysine 36 through Akt Signaling and are Essential for Mouse Embryonic Genome Activation.
Title: Iws1 and Spt6 Regulate Trimethylation of Histone H3 on Lysine 36 through Akt Signaling and are Essential for Mouse Embryonic Genome Activation.
SPT6 facilitates IFN-induced transcription, highlighting its critical role in gene activation.
Title: SPT6 interacts with NSD2 and facilitates interferon-induced transcription.
Iws1 is expressed in all adult organs and it is an essential gene for mouse embryonic development.
Title: Genetic ablation of interacting with Spt6 (Iws1) causes early embryonic lethality.
Biochemical as well as functional experiments revealed that Spt6 could compete for binding of the PRC2 methyltransferase Ezh2 to Suz12 and reduce PRC2 chromatin engagement.
Title: The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins.
These data indicate that, through cooperation with PolII and KDM6A, Spt6 orchestrates removal of H3K27me3, thus controlling developmental gene expression and cell differentiation.
Title: The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis.
Knockdown of Spt6 resulted in severe reduction of class switch recombination in the endogenous Ig locus in B cells.
Title: Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation.
recombinant Spt6 binds selectively to a stretch of uninterrupted consensus repeats located in the N-terminal half of the CTD and recruits Iws1
Title: The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation.
Thus binding of Spt6 to Ser2-P RNAPII provides a cotranscriptional mechanism to recruit Iws1, REF1/Aly, and associated mRNA processing, surveillance, and export factors to responsive genes.
Title: The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export.

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Variation

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Alleles

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

Gene trapped (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_24051-24052:1030022421:1 (e-PCR)
- UniSTS:268837

ksks303 (e-PCR)
- UniSTS:514346

ksks304 (e-PCR)
- UniSTS:514347

Supt6h (e-PCR), detects polymorphism
- UniSTS:479286

AI132449 (e-PCR)
- UniSTS:160126

Supt6h (e-PCR), detects polymorphism
- UniSTS:144524

D11Seg10 (e-PCR), detects polymorphism
- UniSTS:141784

D11Seg11 (e-PCR), detects polymorphism
- UniSTS:141785

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blastocyst formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in nucleobase-containing compound metabolic process	IEA Inferred from Electronic Annotation more info
involved_in nucleosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of isotype switching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription elongation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: transcription elongation factor SPT6

Names: suppressor of Ty 6 homolog

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_009297.2 → NP_033323.2 transcription elongation factor SPT6

See identical proteins and their annotated locations for NP_033323.2

Status: VALIDATED

Source sequence(s)

AK052651, AK136094, AK158846, BC072657

Consensus CDS

CCDS25095.1

UniProtKB/Swiss-Prot

Q5SYM0, Q62383, Q6GQS3, Q6ZQI0, Q8BQY6

Related

ENSMUSP00000002121.5, ENSMUST00000002121.5

Conserved Domains (10) summary

smart00316
Location:1227 → 1282

S1; Ribosomal protein S1-like RNA-binding domain

cd09918
Location:1331 → 1415

SH2_Nterm_SPT6_like; N-terminal Src homology 2 (SH2) domain found in Spt6

cd09928
Location:1424 → 1515

SH2_Cterm_SPT6_like; C-terminal Src homology 2 (SH2) domain found in Spt6

COG2183
Location:372 → 1353

Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]

pfam14639
Location:775 → 931

YqgF; Holliday-junction resolvase-like of SPT6

pfam09371
Location:565 → 623

Tex_N; Tex-like protein N-terminal domain

pfam14633
Location:1304 → 1514

SH2_2; SH2 domain

pfam14635
Location:935 → 1038

HHH_7; Helix-hairpin-helix motif

pfam14641
Location:348 → 422

HTH_44; Helix-turn-helix DNA-binding domain of SPT6

pfam14878
Location:1053 → 1157

DLD; Death-like domain of SPT6

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_000077.7 Reference GRCm39 C57BL/6J

Range

78097575..78136798 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006532743.4 → XP_006532806.1 transcription elongation factor SPT6 isoform X1

Conserved Domains (2) summary

COG2183
Location:249 → 1230

Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]

pfam14633
Location:1181 → 1391

SH2_2; SH2 domain