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    usb1 U6 snRNA biogenesis 1 [ Danio rerio (zebrafish) ]

    Gene ID: 445066, updated on 9-Dec-2024

    Summary

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    Official Symbol
    usb1provided by ZNC
    Official Full Name
    U6 snRNA biogenesis 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040801-197
    See related
    Ensembl:ENSDARG00000003841 AllianceGenome:ZFIN:ZDB-GENE-040801-197
    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
    zgc:91896
    Summary
    Predicted to enable poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends. Acts upstream of or within neutrophil differentiation and regulation of RNA splicing. Predicted to be active in nucleus. Is expressed in several structures, including gonad; head; heart; liver; and pectoral fin. Used to study ablepharon macrostomia syndrome and poikiloderma with neutropenia. Human ortholog(s) of this gene implicated in poikiloderma with neutropenia. Orthologous to human USB1 (U6 snRNA biogenesis phosphodiesterase 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See usb1 in Genome Data Viewer
    Location:
    chromosome: 25
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 25 NC_007136.7 (13677325..13686752)
    105 previous assembly GRCz10 (GCF_000002035.5) 25 NC_007136.6 (13580880..13590352)

    Chromosome 25 - NC_007136.7Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 263 Neighboring gene zinc finger protein 319b Neighboring gene centriolar satellite-associated tubulin polyglutamylase complex regulator 1 Neighboring gene phospholipase A2, group XV Neighboring gene coiled-coil domain containing 135 Neighboring gene lecithin-cholesterol acyltransferase

    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. Deletion of c16orf45 in zebrafish results in a low fertilization rate and increased thigmotaxis. Li T, et al. Dev Psychobiol, 2020 Dec. PMID 32421859
    2. Telomerase RNA-based aptamers restore defective myelopoiesis in congenital neutropenic syndromes. Martínez-Balsalobre E, et al. Nat Commun, 2023 Sep 22. PMID 37737237, Free PMC Article
    3. A zebrafish model of Poikiloderma with Neutropenia recapitulates the human syndrome hallmarks and traces back neutropenia to the myeloid progenitor. Colombo EA, et al. Sci Rep, 2015 Nov 2. PMID 26522474, Free PMC Article
    4. Incomplete splicing of neutrophil-specific genes affects neutrophil development in a zebrafish model of poikiloderma with neutropenia. Patil P, et al. RNA Biol, 2015. PMID 25849198, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deletion of c16orf45 in zebrafish results in a low fertilization rate and increased thigmotaxis.
      Title: Deletion of c16orf45 in zebrafish results in a low fertilization rate and increased thigmotaxis.
    2. USB1 role is modulating the tissue-specific gene splicing that eventually leads to the impaired development of neutrophils.
      Title: Incomplete splicing of neutrophil-specific genes affects neutrophil development in a zebrafish model of poikiloderma with neutropenia.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3'-5'-RNA exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoric diester hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in U6 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within U6 snRNA 3'-end processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in U6 snRNA 3'-end processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in U6 snRNA 3'-end processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neutrophil differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neutrophil differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    U6 snRNA phosphodiesterase 1
    Names
    3'-5' RNA exonuclease USB1
    UPF0406 protein C16orf57 homolog
    putative U6 snRNA phosphodiesterase
    NP_001003460.1
    XP_009296173.1
    XP_009296174.1
    XP_021326153.1

    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_001003460.1 → NP_001003460.1  U6 snRNA phosphodiesterase 1

      See identical proteins and their annotated locations for NP_001003460.1

      Status: PROVISIONAL

      Source sequence(s)
      BC077163
      UniProtKB/Swiss-Prot
      Q6DEF6
      Related
      ENSDARP00000002264.6, ENSDART00000007029.9
      Conserved Domains (1) summary
      pfam09749
      Location:54 → 274
      HVSL; uncharacterized conserved protein

    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_007136.7 Reference GRCz11 Primary Assembly

      Range
      13677325..13686752
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009297899.3 → XP_009296174.1  U6 snRNA phosphodiesterase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AZL1
      Conserved Domains (1) summary
      pfam09749
      Location:1 → 212
      HVSL; Uncharacterized conserved protein

    2. XM_009297898.4 → XP_009296173.1  U6 snRNA phosphodiesterase 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M3APM6
      Conserved Domains (1) summary
      pfam09749
      Location:56 → 276
      HVSL; uncharacterized conserved protein

    3. XM_021470478.2 → XP_021326153.1  U6 snRNA phosphodiesterase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AZL1
      Conserved Domains (1) summary
      pfam09749
      Location:1 → 212
      HVSL; Uncharacterized conserved protein
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6DEF6.1 GenPept UniProtKB/Swiss-Prot:Q6DEF6

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