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    USB1 U6 snRNA biogenesis phosphodiesterase 1 [ Homo sapiens (human) ]

    Gene ID: 79650, updated on 11-Jul-2021

    Summary

    Official Symbol
    USB1provided by HGNC
    Official Full Name
    U6 snRNA biogenesis phosphodiesterase 1provided by HGNC
    Primary source
    HGNC:HGNC:25792
    See related
    Ensembl:ENSG00000103005 MIM:613276
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PN; Mpn1; HVSL1; hUsb1; C16orf57
    Summary
    This gene encodes a protein with several conserved domains, however, its exact function is not known. Mutations in this gene are associated with poikiloderma with neutropenia (PN), which shows phenotypic overlap with Rothmund-Thomson syndrome (RTS) caused by mutations in the RECQL4 gene. It is believed that this gene product interacts with RECQL4 protein via SMAD4 proteins, explaining the partial clinical overlap between PN and RTS. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2011]
    Expression
    Ubiquitous expression in appendix (RPKM 7.3), bone marrow (RPKM 6.0) and 25 other tissues See more
    Orthologs
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    Genomic context

    See USB1 in Genome Data Viewer
    Location:
    16q21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (57999603..58021618)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58033507..58055522)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene cyclic nucleotide gated channel subunit beta 1 Neighboring gene testis, prostate and placenta expressed Neighboring gene Sharpr-MPRA regulatory region 3942 Neighboring gene zinc finger protein 319 Neighboring gene matrix metallopeptidase 15 Neighboring gene TIMELESS interacting protein pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ13154

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in RNA phosphodiester bond hydrolysis, exonucleolytic IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in U6 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in U6 snRNA 3'-end processing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in U6 snRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in snRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    U6 snRNA phosphodiesterase
    Names
    HVSL motif containing 1
    U six biogenesis 1
    U6 snRNA biogenesis 1
    UPF0406 protein C16orf57
    mutated in poikiloderma with neutropenia protein 1
    putative U6 snRNA phosphodiesterase
    NP_001182231.1
    NP_001191840.1
    NP_001317497.1
    NP_001317498.1
    NP_078874.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_027698.1 RefSeqGene

      Range
      5001..25251
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_352

    mRNA and Protein(s)

    1. NM_001195302.2NP_001182231.1  U6 snRNA phosphodiesterase isoform 2

      See identical proteins and their annotated locations for NP_001182231.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AC012182, AK303121, DB364698, DC363309
      Consensus CDS
      CCDS55998.1
      UniProtKB/Swiss-Prot
      Q9BQ65
      Related
      ENSP00000446143.2, ENST00000539737.6
      Conserved Domains (1) summary
      pfam09749
      Location:44245
      HVSL; uncharacterized conserved protein
    2. NM_001204911.2NP_001191840.1  U6 snRNA phosphodiesterase isoform 3

      See identical proteins and their annotated locations for NP_001191840.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks several exons from the 3' end, and contains an alternate 3' terminal exon compared to variant 1. This results in a shorter isofom (3) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC010543, AK301494, BF733890, BI910866, BQ223186, BX117268, DB382938, DC380401
      Consensus CDS
      CCDS55997.1
      UniProtKB/Swiss-Prot
      Q9BQ65
      Related
      ENSP00000409792.3, ENST00000423271.7
      Conserved Domains (1) summary
      pfam09749
      Location:44151
      HVSL; uncharacterized conserved protein
    3. NM_001330568.2NP_001317497.1  U6 snRNA phosphodiesterase isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate 5' terminal exon, resulting in a distinct 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC012182, BC007774, DC386004
      Consensus CDS
      CCDS81991.1
      UniProtKB/Swiss-Prot
      Q9BQ65
      UniProtKB/TrEMBL
      H3BNM8
      Related
      ENSP00000454928.1, ENST00000561743.5
      Conserved Domains (1) summary
      pfam09749
      Location:1212
      HVSL; uncharacterized conserved protein
    4. NM_001330569.2NP_001317498.1  U6 snRNA phosphodiesterase isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks several exons in the 3' coding region, and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC010543
      Consensus CDS
      CCDS81990.1
      UniProtKB/TrEMBL
      H3BN52
      Related
      ENSP00000454692.1, ENST00000563149.1
      Conserved Domains (1) summary
      pfam09749
      Location:44149
      HVSL; uncharacterized conserved protein
    5. NM_024598.4NP_078874.2  U6 snRNA phosphodiesterase isoform 1

      See identical proteins and their annotated locations for NP_078874.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC012182, BC004415, DB364698, DC363309
      Consensus CDS
      CCDS10791.1
      UniProtKB/Swiss-Prot
      Q9BQ65
      UniProtKB/TrEMBL
      A0A024R6V6
      Related
      ENSP00000219281.3, ENST00000219281.8
      Conserved Domains (1) summary
      pfam09749
      Location:44263
      HVSL; Uncharacterized conserved protein

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

      Range
      57999603..58021618
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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