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

    Gene ID: 79650, updated on 8-Oct-2017
    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; Vega:OTTHUMG00000133456
    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]
    Orthologs
    Location:
    16q21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 16 NC_000016.10 (57999600..58021623)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58033450..58055527)

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

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ13154

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    3'-5'-exoribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA phosphodiester bond hydrolysis, exonucleolytic IEA
    Inferred from Electronic Annotation
    more info
     
    RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    U6 snRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    intercellular bridge IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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_078874.2
    XP_005256201.1
    XP_011521630.1
    XP_011521631.1
    XP_011521632.1

    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_001195302.1NP_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, OTTHUMP00000253648, ENST00000539737.6, OTTHUMT00000429947
      Conserved Domains (1) summary
      pfam09749
      Location:44245
      HVSL; uncharacterized conserved protein
    2. NM_001204911.1NP_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, OTTHUMP00000253649, ENST00000423271.7, OTTHUMT00000429948
      Conserved Domains (1) summary
      pfam09749
      Location:44151
      HVSL; uncharacterized conserved protein
    3. NM_001330568.1NP_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
      Conserved Domains (1) summary
      pfam09749
      Location:1212
      HVSL; uncharacterized conserved protein
    4. NM_001330569.1NP_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
      Conserved Domains (1) summary
      pfam09749
      Location:44149
      HVSL; uncharacterized conserved protein
    5. NM_024598.3NP_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, OTTHUMP00000164660, ENST00000219281.7, OTTHUMT00000257331
      Conserved Domains (1) summary
      pfam09749
      Location:44263
      HVSL; Uncharacterized conserved protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 Primary Assembly

      Range
      57999600..58021623
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005256144.3XP_005256201.1  U6 snRNA phosphodiesterase isoform X2

      Related
      ENSP00000454928.1, OTTHUMP00000253647, ENST00000561743.5, OTTHUMT00000429946
      Conserved Domains (1) summary
      pfam09749
      Location:1212
      HVSL; uncharacterized conserved protein
    2. XM_011523329.2XP_011521631.1  U6 snRNA phosphodiesterase isoform X2

      See identical proteins and their annotated locations for XP_011521631.1

      UniProtKB/TrEMBL
      H3BNM8
      Conserved Domains (1) summary
      pfam09749
      Location:1212
      HVSL; uncharacterized conserved protein
    3. XM_011523328.2XP_011521630.1  U6 snRNA phosphodiesterase isoform X1

      Conserved Domains (1) summary
      pfam09749
      Location:31250
      HVSL; uncharacterized conserved protein
    4. XM_011523330.1XP_011521632.1  U6 snRNA phosphodiesterase isoform X3

      Related
      ENSP00000454692.1, OTTHUMP00000253650, ENST00000563149.1, OTTHUMT00000429953
      Conserved Domains (1) summary
      pfam09749
      Location:44149
      HVSL; uncharacterized conserved protein

    RNA

    1. XR_933427.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      59442351..59462601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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