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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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