Display Settings:

Format

Send to:

Choose Destination

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

Gene ID: 79650, updated on 22-Nov-2014
Official Symbol
USB1provided by HGNC
Official Full Name
U6 snRNA biogenesis 1provided by HGNC
Primary source
HGNC:HGNC:25792
See related
Ensembl:ENSG00000103005; HPRD:07815; 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]
See USB1 in Epigenomics, MapViewer
Location:
16q21
Exon count:
9
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 16 NC_000016.10 (57999605..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 kinesin family member C3 Neighboring gene uncharacterized LOC388282 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 (membrane-inserted) Neighboring gene TIMELESS interacting protein pseudogene

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 IDA
Inferred from Direct Assay
more info
PubMed 
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
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
U6 snRNA phosphodiesterase
Names
U6 snRNA phosphodiesterase
USB1
U six biogenesis 1
HVSL motif containing 1
UPF0406 protein C16orf57
putative U6 snRNA phosphodiesterase
mutated in poikiloderma with neutropenia protein 1
NP_001182231.1
NP_001191840.1
NP_078874.2

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 

    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 proteins identical to 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
    Conserved Domains (1) summary
    pfam09749
    Location:44246
    HVSL; Uncharacterized conserved protein
  2. NM_001204911.1NP_001191840.1  U6 snRNA phosphodiesterase isoform 3

    See proteins identical to 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
    Conserved Domains (1) summary
    pfam09749
    Location:44147
    HVSL; Uncharacterized conserved protein
  3. NM_024598.3NP_078874.2  U6 snRNA phosphodiesterase isoform 1

    See proteins identical to 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/TrEMBL
    A0A024R6V6
    UniProtKB/Swiss-Prot
    Q9BQ65
    Related
    ENSP00000219281, OTTHUMP00000164660, ENST00000219281, OTTHUMT00000257331
    Conserved Domains (1) summary
    pfam09749
    Location:44264
    HVSL; Uncharacterized conserved protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Alternate HuRef

Genomic

  1. AC_000148.1 

    Range
    43902322..43922661
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000016.10 

    Range
    57999605..58021623
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256144.2XP_005256201.1  

    UniProtKB/TrEMBL
    H3BNM8
    Conserved Domains (1) summary
    pfam09749
    Location:1213
    HVSL; Uncharacterized conserved protein

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 

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