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

Gene ID: 64275, updated on 11-Apr-2024

Summary

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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 from RNA polymerase II promoter. Located in nucleus. Is expressed in brain and optic cup. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See supt5h in Genome Data Viewer
Location:
chromosome: 15
Exon count:
31
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (20364564..20395252)
105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (20428652..20459520)

Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain containing, family G (with RhoGef domain) member 2 Neighboring gene interleukin 15, like Neighboring gene uncharacterized LOC110437902 Neighboring gene ribonuclease T2, like Neighboring gene cytochrome c oxidase subunit 7A1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The elongation factors Pandora/Spt6 and Foggy/Spt5 promote transcription in the zebrafish embryo. Keegan BR, et al. Development, 2002 Apr. PMID 11923199
  2. A regulator of transcriptional elongation controls vertebrate neuronal development. Guo S, et al. Nature, 2000 Nov 16. PMID 11099044
  3. Zebrafish foggy/spt 5 is required for migration of facial branchiomotor neurons but not for their survival. Cooper KL, et al. Dev Dyn, 2005 Nov. PMID 16193504, Free PMC Article
  4. Repression of RNA polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5. Chen H, et al. PLoS One, 2009 Sep 9. PMID 19742326, Free PMC Article
  5. Mutations in the zebrafish unmask shared regulatory pathways controlling the development of catecholaminergic neurons. Guo S, et al. Dev Biol, 1999 Apr 15. PMID 10191060

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

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
  
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)

  1. 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

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007126.7 Reference GRCz11 Primary Assembly

    Range
    20364564..20395252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005157529.4 → XP_005157586.1  transcription elongation factor SPT5 isoform X1

    See identical proteins and their annotated locations for XP_005157586.1

    UniProtKB/Swiss-Prot
    Q6PFJ3, Q9DDT5
    UniProtKB/TrEMBL
    A0A8M9Q0J3
    Conserved Domains (5) summary
    cd09888
    Location:179 → 266
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    cd06081
    Location:277 → 314
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    cl26303
    Location:335 → 965
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

  2. XM_021481462.1 → XP_021337137.1  transcription elongation factor SPT5 isoform X1

    UniProtKB/Swiss-Prot
    Q6PFJ3, Q9DDT5
    UniProtKB/TrEMBL
    A0A8M9Q0J3
    Conserved Domains (5) summary
    cd09888
    Location:179 → 266
    NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
    cd06081
    Location:277 → 314
    KOW_Spt5_1; KOW domain of Spt5, repeat 1
    cd06086
    Location:1028 → 1084
    KOW_Spt5_6; KOW domain of Spt5, repeat 6
    pfam11942
    Location:93 → 172
    Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    cl26303
    Location:335 → 965
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

  3. XM_021481463.1 → XP_021337138.1  transcription elongation factor SPT5 isoform X2

    UniProtKB/Swiss-Prot
    Q6PFJ3, Q9DDT5
    UniProtKB/TrEMBL
    A0A8M1P6F8, F1QD27
    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

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394946.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    268691..296756
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9DDT5.1 GenPept UniProtKB/Swiss-Prot:Q9DDT5

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