Supt5 suppressor of Ty 5, DSIF elongation factor subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Supt5provided by MGI
Official Full Name: suppressor of Ty 5, DSIF elongation factor subunitprovided by MGI
Primary source: MGI:MGI:1202400
See related: Ensembl:ENSMUSG00000003435 AllianceGenome:MGI:1202400
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: Spt5; Supt5h
Summary: Enables chromatin binding activity. Predicted to be involved in positive regulation of macroautophagy; regulation of RNA metabolic process; and transcription elongation from RNA polymerase II promoter. Predicted to be located in nucleoplasm. Predicted to be part of DSIF complex. Is expressed in several structures, including genitourinary system; limb mesenchyme; and nervous system. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 68.8), adrenal adult (RPKM 67.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A3; 7 16.68 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (28014316..28038341, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (28314891..28338804, complement)

Chromosome 7 - NC_000073.7 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: 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?

SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
Title: SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15-20 kb from the promoter.
Title: Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.
Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo-activated cells.
Title: Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo-activated cells.
our findings indicate that Spt4 and Spt5 have essential functions in the DNA repair phase of immunoglobulin class switch recombination.
Title: The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination.
Study reports that Spt5, a factor normally associated with stalled or paused Pol II, is required for class switch recombination.
Title: Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5.

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Variation

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Alleles

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

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

RH124224 (e-PCR)
- UniSTS:161046

RH136432 (e-PCR)
- UniSTS:210419

RH124190 (e-PCR)
- UniSTS:161012

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription, elongation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription, elongation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription elongation-coupled chromatin remodeling	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DSIF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DSIF complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription elongation factor SPT5

Names: DRB sensitivity-inducing factor large subunit; DSIF large subunit; suppressor of Ty 5 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_001417308.1 → NP_001404237.1 transcription elongation factor SPT5 isoform b

Status: VALIDATED

Source sequence(s)

AC148986
NM_001417309.1 → NP_001404238.1 transcription elongation factor SPT5 isoform b

Status: VALIDATED

Source sequence(s)

AC148986

Related

ENSMUST00000207879.2
NM_001417310.1 → NP_001404239.1 transcription elongation factor SPT5 isoform c

Status: VALIDATED

Source sequence(s)

AC148986
NM_013676.2 → NP_038704.1 transcription elongation factor SPT5 isoform a

See identical proteins and their annotated locations for NP_038704.1

Status: VALIDATED

Source sequence(s)

AC148986

Consensus CDS

CCDS39857.1

UniProtKB/Swiss-Prot

O55201, Q3UJ77, Q3UJH1, Q3UKD7, Q3UM54, Q6PB73, Q6PDP0, Q6PFR4

Related

ENSMUSP00000003527.9, ENSMUST00000003527.10

Conserved Domains (12) summary

PRK08559
Location:173 → 314

nusG; transcription antitermination protein NusG; Validated

cd09888
Location:176 → 263

NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)

COG5164
Location:332 → 959

SPT5; Transcription elongation factor [Transcription]

cd06081
Location:274 → 311

KOW_Spt5_1; KOW domain of Spt5, repeat 1

cd06082
Location:418 → 468

KOW_Spt5_2; KOW domain of Spt5, repeat 2

cd06083
Location:469 → 519

KOW_Spt5_3; KOW domain of Spt5, repeat 3

cd06084
Location:595 → 637

KOW_Spt5_4; KOW domain of Spt5, repeat 4

cd06085
Location:696 → 745

KOW_Spt5_5; KOW domain of Spt5, repeat 5

cd06086
Location:1022 → 1079

KOW_Spt5_6; KOW domain of Spt5, repeat 6

pfam04731
Location:841 → 970

Caudal_act; Caudal like protein activation region

pfam11942
Location:91 → 169

Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

pfam12815
Location:760 → 816

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

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

28014316..28038341 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006539703.3 → XP_006539766.1 transcription elongation factor SPT5 isoform X2

Conserved Domains (5) summary

cd09888
Location:176 → 263

NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)

COG5164
Location:332 → 906

SPT5; Transcription elongation factor [Transcription]

cd06081
Location:274 → 311

KOW_Spt5_1; KOW domain of Spt5, repeat 1

cd06086
Location:969 → 1026

KOW_Spt5_6; KOW domain of Spt5, repeat 6

pfam11942
Location:73 → 169

Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
XM_036152859.1 → XP_036008752.1 transcription elongation factor SPT5 isoform X3

Conserved Domains (4) summary

cd09888
Location:37 → 124

NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)

COG5164
Location:193 → 820

SPT5; Transcription elongation factor [Transcription]

cd06081
Location:135 → 172

KOW_Spt5_1; KOW domain of Spt5, repeat 1

cd06086
Location:883 → 940

KOW_Spt5_6; KOW domain of Spt5, repeat 6