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    ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component [ Danio rerio (zebrafish) ]

    Gene ID: 100036549, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ctr9provided by ZNC
    Official Full Name
    CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-3782
    See related
    Ensembl:ENSDARG00000009170 AllianceGenome:ZFIN:ZDB-GENE-030131-3782
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fc54a06; wu:fc54a06
    Summary
    Predicted to enable RNA polymerase II complex binding activity. Involved in heart development. Acts upstream of or within neural crest cell development; pigmentation; and somitogenesis. Located in nucleus. Part of Cdc73/Paf1 complex. Orthologous to human CTR9 (CTR9 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ctr9 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (66655729..66693712, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (66432081..66470064, complement)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene transmembrane protein 176l.3b Neighboring gene eukaryotic translation initiation factor 4, gamma 2a Neighboring gene inositol 1,4,5-triphosphate receptor associated 2-like Neighboring gene uncharacterized LOC137496106

    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. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Hill JT, et al. Genome Res, 2013 Apr. PMID 23299975, Free PMC Article
    2. The PAF1 complex differentially regulates cardiomyocyte specification. Langenbacher AD, et al. Dev Biol, 2011 May 1. PMID 21338598, Free PMC Article
    3. Paf1 complex homologues are required for Notch-regulated transcription during somite segmentation. Akanuma T, et al. EMBO Rep, 2007 Sep. PMID 17721442, Free PMC Article
    4. The Paf1 complex and P-TEFb have reciprocal and antagonist roles in maintaining multipotent neural crest progenitors. Jurynec MJ, et al. Development, 2019 Dec 16. PMID 31784460, Free PMC Article
    5. TIF1gamma controls erythroid cell fate by regulating transcription elongation. Bai X, et al. Cell, 2010 Jul 9. PMID 20603019, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural crest cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within pigmentation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within somitogenesis 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
    		  
    Component Evidence Code Pubs
    part_of Cdc73/Paf1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Cdc73/Paf1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA polymerase-associated protein CTR9 homolog
    Names
    Ctr9, Paf1/RNA polymerase II complex component, 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)

    1. NM_001083583.1 → NP_001077052.1  RNA polymerase-associated protein CTR9 homolog

      See identical proteins and their annotated locations for NP_001077052.1

      Status: PROVISIONAL

      Source sequence(s)
      AB286670
      UniProtKB/TrEMBL
      A0A8M1NCG2, A3KDM3
      Related
      ENSDARP00000016047.7, ENSDART00000021317.10
      Conserved Domains (6) summary
      TIGR02795
      Location:310 → 414
      tol_pal_ybgF; tol-pal system protein YbgF
      sd00006
      Location:501 → 525
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:165 → 228
      TPR_11; TPR repeat
      pfam13424
      Location:498 → 563
      TPR_12; Tetratricopeptide repeat
      pfam14559
      Location:691 → 750
      TPR_19; Tetratricopeptide repeat
      pfam14797
      Location:1029 → 1153
      SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007118.7 Reference GRCz11 Primary Assembly

      Range
      66655729..66693712 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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