SPT5 transcription elongation factor SPT5 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SPT5
Official Full Name: transcription elongation factor SPT5
Primary source: SGD:S000004470
Locus tag: YML010W
See related: AllianceGenome:SGD:S000004470; FungiDB:YML010W; VEuPathDB:YML010W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables several functions, including RNA polymerase I general transcription initiation factor binding activity; RNA polymerase core enzyme binding activity; and nucleic acid binding activity. Contributes to single-stranded RNA binding activity. Involved in several processes, including positive regulation of autophagy; regulation of nucleobase-containing compound metabolic process; and spliceosomal complex assembly. Located in nucleus and rDNA heterochromatin. Part of DSIF complex. Is active in chromatin. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See SPT5 in Genome Data Viewer

Location:: chromosome: XIII

Exon count:: 1

Sequence:: Chromosome: XIII; NC_001145.3 (247677..250868)

Chromosome XIII - NC_001145.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001145.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spt5 orchestrates cryptic transcript suppression and transcriptional directionality.
Title: Spt5 orchestrates cryptic transcript suppression and transcriptional directionality.
Emerging Roles of SPT5 in Transcription.
Title: Emerging Roles of SPT5 in Transcription.
Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures.
Title: Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures.
Structural basis of nucleosome transcription mediated by Chd1 and FACT.
Title: Structural basis of nucleosome transcription mediated by Chd1 and FACT.
Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription.
Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription.
Transcriptional nucleotide misincorporation is not implicated in TC-NER, and moderate eviction of Spt5 and promotion of error-free transcriptional bypass of DNA lesions by Rad26 facilitates TC-NER.
Title: Evidence that Moderate Eviction of Spt5 and Promotion of Error-Free Transcriptional Bypass by Rad26 Facilitates Transcription Coupled Nucleotide Excision Repair.
All together, our results reveal an important role of Rpb5 in the transition from initiation to elongation mediated by the RNA polymerase II, by modulating the Spt5 association, and the backtracking activity of the enzyme.
Title: Rpb5 modulates the RNA polymerase II transition from initiation to elongation by influencing Spt5 association and backtracking.
Interactions between SPT5 and RNA Polymerase II
Title: Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae.
Spt4/5 may be important to coordinate the mechanical movement of RNAPII through the nucleosome with co-transcriptional chromatin modifications during transcription.
Title: The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome.
Spt5 is crucial for a normal rate of RNA synthesis and distribution of RNAPII over transcription units.
Title: Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase I core binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase I general transcription initiation factor binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II complex binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables U1 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U2 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U4 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U5 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U6 snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables rRNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables snRNP binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular mRNA localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription elongation by RNA polymerase I	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
involved_in regulation of rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription-coupled nucleotide-excision repair	IGI Inferred from Genetic Interaction more info	PubMed
involved_in spliceosomal complex assembly	IDA Inferred from Direct Assay 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	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	IPI Inferred from Physical Interaction more info	PubMed
is_active_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in intracellular membraneless organelle	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
located_in rDNA heterochromatin	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcription elongation factor SPT5

NP_013703.1

Spt4p/5p (DSIF) transcription elongation factor complex subunit; the Spt4/5 complex binds to ssRNA in a sequence-specific manner, and in concert with RNAP I and II has multiple roles regulating transcriptional elongation, RNA processing, quality control, and transcription-coupled repair; interacts with DNA upstream of RNAPII and the non-template strand of the transcription bubble; Spt5p is the only transcription elongation factor conserved in all domains of life

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_001145.3 Reference assembly

Range

247677..250868

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182366.1 → NP_013703.1 TPA: transcription elongation factor SPT5 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013703.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VZG4, P27692

UniProtKB/TrEMBL

A6ZM52, G2WK42, N1NY50

Conserved Domains (5) summary

cd09888
Location:287 → 373

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

COG5164
Location:441 → 1059

SPT5; Transcription elongation factor [Transcription]

PRK08581
Location:2 → 142

PRK08581; amidase domain-containing protein

cd06081
Location:385 → 422

KOW_Spt5_1; KOW domain of Spt5, repeat 1

pfam11942
Location:180 → 280

Spt5_N; Spt5 transcription elongation factor, acidic N-terminal