supt5h SPT5 homolog, DSIF elongation factor subunit [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: supt5hprovided by ZNC
Official Full Name: SPT5 homolog, DSIF elongation factor subunitprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001207-1
See related: Ensembl:ENSDARG00000042724 AllianceGenome:ZFIN:ZDB-GENE-001207-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fog; Spt5; foggy; fb37g01; fb95e05; wu:fb37g01; wu:fb95e05; wu:fc10f02; etID10129.15; etID37101.15
Summary: Enables DNA binding activity. Acts upstream of or within several processes, including generation of neurons; regulation of signal transduction; and regulation of transcription elongation by RNA polymerase II. Located in nucleus. Is expressed in brain; optic cup; and telencephalon. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 15

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	15	NC_007126.7 (20364605..20395252)
105	previous assembly	GRCz10 (GCF_000002035.5)	15	NC_007126.6 (20428652..20459520)

Chromosome 15 - NC_007126.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the positive function of Foggy/Spt5 is required for gata1 expression during zebrafish embryonic hematopoiesis.
Title: Erythropoiesis is regulated by the transcription elongation factor Foggy/Spt5 through gata1 gene regulation.
RNA polymerase II elongation repression is critically dependent on the C-terminus of Spt5
Title: Repression of RNA polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5.
Spt5 as a dual regulator of transcription elongation in vivo; a small but diverse set of target genes critically dependent on Spt5 during development.
Title: Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo.
spt 5-dependent transcript elongation is required cell-autonomously for a complex cell migration
Title: Zebrafish foggy/spt 5 is required for migration of facial branchiomotor neurons but not for their survival.
The elongation factors Pandora/Spt6 and Foggy/Spt5 promote transcription in the zebrafish embryo.
Title: The elongation factors Pandora/Spt6 and Foggy/Spt5 promote transcription in the zebrafish embryo.

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General gene information

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Markers

fi18f11.x1 (e-PCR)
- UniSTS:196959

fb95e05.x1 (e-PCR)
- UniSTS:191882

fb95e05.x1 (e-PCR)
- UniSTS:191883

fc10f02.x1 (e-PCR)
- UniSTS:192465

AI437093 (e-PCR)
- UniSTS:206591

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables translation elongation factor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within central nervous system neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of fibroblast growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of receptor signaling pathway via JAK-STAT	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of type II interferon-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription elongation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	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
acts_upstream_of_or_within transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within transcription elongation-coupled chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within translation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within translational elongation	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	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation 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; protein foggy; suppressor of Ty 5 homolog; transcription elongation regulator foggy

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_131673.2 → NP_571748.2 transcription elongation factor SPT5

Status: VALIDATED

Source sequence(s)

CR626887

UniProtKB/Swiss-Prot

Q6PFJ3, Q9DDT5

UniProtKB/TrEMBL

A0A8M1P6F8, F1QD27

Related

ENSDARP00000062675.6, ENSDART00000062676.8

Conserved Domains (5) summary

cd09888
Location:177 → 264

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

cd06081
Location:275 → 312

KOW_Spt5_1; KOW domain of Spt5, repeat 1

cd06086
Location:1026 → 1082

KOW_Spt5_6; KOW domain of Spt5, repeat 6

pfam11942
Location:92 → 170

Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

cl26303
Location:333 → 963

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4