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    Usb1 U6 snRNA biogenesis 1 [ Mus musculus (house mouse) ]

    Gene ID: 101985, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Usb1provided by MGI
    Official Full Name
    U6 snRNA biogenesis 1provided by MGI
    Primary source
    MGI:MGI:2142454
    See related
    Ensembl:ENSMUSG00000031792 AllianceGenome:MGI:2142454
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Predicted to enable poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends. Predicted to be involved in RNA splicing and U6 snRNA 3'-end processing. Predicted to be located in intercellular bridge and nucleoplasm. Predicted to be active in nucleus. 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]
    Expression
    Ubiquitous expression in thymus adult (RPKM 14.6), ovary adult (RPKM 13.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Usb1 in Genome Data Viewer
    Location:
    8 C5; 8 47.12 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (96058006..96074137)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (95331413..95347513)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene microtubule-associated protein 1 light chain 3 pseudogene copy 6 Neighboring gene sperm microtubule inner protein 8 Neighboring gene STARR-positive B cell enhancer ABC_E8259 Neighboring gene zinc finger protein 319 Neighboring gene matrix metallopeptidase 15 Neighboring gene VISTA enhancer mm71 Neighboring gene cilia and flagella associated protein 20 Neighboring gene STARR-positive B cell enhancer ABC_E245

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
    2. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article
    3. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    4. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article
    5. Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Zambrowicz BP, et al. Proc Natl Acad Sci U S A, 2003 Nov 25. PMID 14610273, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 3'-5'-RNA exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends ISO
    Inferred from Sequence Orthology
    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 RNA splicing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in RNA splicing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in U6 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in U6 snRNA 3'-end processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in U6 snRNA 3'-end processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in snRNA 3'-end processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in snRNA 3'-end processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in intercellular bridge ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    U6 snRNA phosphodiesterase 1
    Names
    3'-5' RNA exonuclease USB1
    U6 snRNA phosphodiesterase
    UPF0406 protein C16orf57 homolog
    putative U6 snRNA phosphodiesterase
    NP_001413481.1
    NP_001413482.1
    NP_598715.2
    XP_017167985.1

    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_001426552.1 → NP_001413481.1  U6 snRNA phosphodiesterase 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC165414
      UniProtKB/Swiss-Prot
      Q3TU91, Q91W78

    2. NM_001426553.1 → NP_001413482.1  U6 snRNA phosphodiesterase 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC165414
      UniProtKB/Swiss-Prot
      Q3TU91, Q91W78

    3. NM_133954.3 → NP_598715.2  U6 snRNA phosphodiesterase 1 isoform 1

      See identical proteins and their annotated locations for NP_598715.2

      Status: VALIDATED

      Source sequence(s)
      AC165414
      Consensus CDS
      CCDS22560.1
      UniProtKB/Swiss-Prot
      Q3TU91, Q91W78
      UniProtKB/TrEMBL
      A0A0R4J0E0
      Related
      ENSMUSP00000034245.9, ENSMUST00000034245.16
      Conserved Domains (1) summary
      pfam09749
      Location:45 → 265
      HVSL; Uncharacterized conserved protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000074.7 Reference GRCm39 C57BL/6J

      Range
      96058006..96074137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017312496.3 → XP_017167985.1  U6 snRNA phosphodiesterase 1 isoform X1

      UniProtKB/Swiss-Prot
      Q3TU91, Q91W78
      UniProtKB/TrEMBL
      A0A0R4J0E0
      Conserved Domains (1) summary
      pfam09749
      Location:45 → 265
      HVSL; Uncharacterized conserved protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91W78.1 GenPept UniProtKB/Swiss-Prot:Q91W78

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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