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Aliases for USB1 Gene

Aliases for USB1 Gene

  • U6 SnRNA Biogenesis 1 2 3
  • C16orf57 3 4 6
  • Mutated In Poikiloderma With Neutropenia Protein 1 2 3
  • HVSL Motif Containing 1 2 3
  • U Six Biogenesis 1 2 3
  • HUsb1 3 4
  • PN 3 6
  • Chromosome 16 Open Reading Frame 57 2
  • Putative U6 SnRNA Phosphodiesterase 3
  • Poikiloderma With Neutropenia 2
  • U6 SnRNA Phosphodiesterase 3
  • UPF0406 Protein C16orf57 3
  • EC 3.1.4.- 4
  • HVSL1 3
  • Mpn1 3

External Ids for USB1 Gene

Previous Symbols for USB1 Gene

  • C16orf57

Summaries for USB1 Gene

Entrez Gene Summary for USB1 Gene

  • 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]

GeneCards Summary for USB1 Gene

USB1 (U6 SnRNA Biogenesis 1) is a Protein Coding gene. Diseases associated with USB1 include poikiloderma with neutropenia and rothmund-thomson syndrome. GO annotations related to this gene include 3-5-exoribonuclease activity.

UniProtKB/Swiss-Prot for USB1 Gene

  • Phosphodiesterase responsible for the U6 snRNA 3 end processing. Acts as an exoribonuclease (RNase) responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the formation of mature U6 snRNA 3 end-terminated with a 2,3-cyclic phosphate.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USB1 Gene

Genomics for USB1 Gene

Genomic Location for USB1 Gene

57,999,546 bp from pter
58,021,623 bp from pter
22,078 bases
Plus strand

Genomic View for USB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for USB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USB1 Gene

No data available for Regulatory Elements for USB1 Gene

Proteins for USB1 Gene

  • Protein details for USB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    U6 snRNA phosphodiesterase
    Protein Accession:
    Secondary Accessions:
    • B4DWE3
    • B4DZW5
    • Q96FZ9
    • Q9H8X8

    Protein attributes for USB1 Gene

    265 amino acids
    Molecular mass:
    30268 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for USB1 Gene

    Alternative splice isoforms for USB1 Gene


neXtProt entry for USB1 Gene

Proteomics data for USB1 Gene at MOPED

Post-translational modifications for USB1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USB1 Gene

Domains for USB1 Gene

Protein Domains for USB1 Gene



  • Belongs to the 2H phosphoesterase superfamily. USB1 family.:
    • Q9BQ65
genes like me logo Genes that share domains with USB1: view

No data available for Gene Families for USB1 Gene

Function for USB1 Gene

Molecular function for USB1 Gene

UniProtKB/Swiss-Prot Function: Phosphodiesterase responsible for the U6 snRNA 3 end processing. Acts as an exoribonuclease (RNase) responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the formation of mature U6 snRNA 3 end-terminated with a 2,3-cyclic phosphate.

Enzyme Numbers (IUBMB) for USB1 Gene

Gene Ontology (GO) - Molecular Function for USB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3-5-exoribonuclease activity IDA 23190533
GO:0004518 nuclease activity --
genes like me logo Genes that share ontologies with USB1: view
genes like me logo Genes that share phenotypes with USB1: view

miRNA for USB1 Gene

miRTarBase miRNAs that target USB1

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for USB1 Gene

Localization for USB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USB1 Gene

Gene Ontology (GO) - Cellular Components for USB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 22899009
genes like me logo Genes that share ontologies with USB1: view

Pathways for USB1 Gene

SuperPathways for USB1 Gene

No Data Available

Interacting Proteins for USB1 Gene

Gene Ontology (GO) - Biological Process for USB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IMP 22899009
GO:0034477 U6 snRNA 3-end processing IMP 22899009
GO:0090305 nucleic acid phosphodiester bond hydrolysis --
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic IDA 23190533
genes like me logo Genes that share ontologies with USB1: view

No data available for Pathways by source for USB1 Gene

Transcripts for USB1 Gene

Unigene Clusters for USB1 Gene

U6 snRNA biogenesis 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USB1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b
SP1: - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - -
SP5: - - -
SP6: - - -
SP7: - - - -
SP8: - - - - - - - -

Relevant External Links for USB1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USB1 Gene

mRNA expression in normal human tissues for USB1 Gene

mRNA differential expression in normal tissues according to GTEx for USB1 Gene

This gene is overexpressed in Whole Blood (9.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for USB1 Gene

SOURCE GeneReport for Unigene cluster for USB1 Gene Hs.408702

genes like me logo Genes that share expressions with USB1: view

Orthologs for USB1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for USB1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C16ORF57 37
  • 98 (a)
USB1 36
  • 99.5 (n)
  • 98.49 (a)
(Bos Taurus)
Mammalia USB1 36
  • 86.92 (n)
  • 83.77 (a)
USB1 37
  • 84 (a)
(Canis familiaris)
Mammalia USB1 36
  • 86.11 (n)
  • 83.33 (a)
USB1 37
  • 59 (a)
(Mus musculus)
Mammalia Usb1 36
  • 83.4 (n)
  • 81.13 (a)
Usb1 16
Usb1 37
  • 81 (a)
(Monodelphis domestica)
Mammalia USB1 37
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia USB1 37
  • 71 (a)
(Rattus norvegicus)
Mammalia Usb1 36
  • 84.15 (n)
  • 83.4 (a)
(Gallus gallus)
Aves C11H16ORF57 36
  • 71.55 (n)
  • 65.97 (a)
USB1 37
  • 69 (a)
(Anolis carolinensis)
Reptilia USB1 37
  • 64 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC52944 36
tropical clawed frog
(Silurana tropicalis)
Amphibia usb1 36
  • 61.62 (n)
  • 55.41 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2636 36
(Danio rerio)
Actinopterygii usb1 36
  • 58.93 (n)
  • 50.45 (a)
usb1 37
  • 46 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002220 36
  • 49.43 (n)
  • 38.54 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG16790 36
  • 51.37 (n)
  • 42.78 (a)
CG16790 37
  • 36 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G51170 36
  • 45.49 (n)
  • 39.06 (a)
(Oryza sativa)
Liliopsida Os02g0651000 36
  • 40.79 (n)
  • 32.17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 26 (a)
Species with no ortholog for USB1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for USB1 Gene

Gene Tree for USB1 (if available)
Gene Tree for USB1 (if available)

Paralogs for USB1 Gene

No data available for Paralogs for USB1 Gene

Variants for USB1 Gene

Sequence variations from dbSNP and Humsavar for USB1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs194100 -- 58,012,270(-) AATGA(C/G)AATCC intron-variant, utr-variant-3-prime
rs194101 -- 58,012,064(-) TTTGG(C/G)TAGAA intron-variant, utr-variant-3-prime
rs194102 -- 58,012,046(-) TATTT(C/T)TGTTT intron-variant, utr-variant-3-prime
rs194103 -- 58,009,031(-) atata(A/T)aagac intron-variant
rs194104 -- 58,008,934(-) acttg(A/G)agatt intron-variant

Relevant External Links for USB1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Structural Variations from Database of Genomic Variants (DGV) for USB1 Gene

Disorders for USB1 Gene

(1) OMIM Diseases for USB1 Gene (613276)


  • Poikiloderma with neutropenia (PN) [MIM:604173]: A genodermatosis characterized by poikiloderma, pachyonychia and chronic neutropenia. The disorder starts as a papular erythematous rash on the limbs during the first year of life. It gradually spreads centripetally and, as the papular rash resolves, hypo- and hyperpigmentation result, with development of telangiectasias. Another skin manifestation is pachyonychia, but alopecia and leukoplakia are distinctively absent. Patients have recurrent pneumonias that usually result in reactive airway disease and/or chronic cough. One of the most important extracutaneous symptoms is an increased susceptibility to infections, mainly affecting the respiratory system, primarily due to a chronic neutropenia and to neutrophil functional defects. Bone marrow abnormalities account for neutropenia and may evolve into myelodysplasia associated with the risk of leukemic transformation. Poikiloderma with neutropenia shows phenotypic overlap with Rothmund-Thomson syndrome. {ECO:0000269 PubMed:20004881, ECO:0000269 PubMed:20503306}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with USB1: view

Publications for USB1 Gene

  1. Targeted next-generation sequencing appoints c16orf57 as clericuzio- type poikiloderma with neutropenia gene. (PMID: 20004881) Volpi L. … Larizza L. (Am. J. Hum. Genet. 2010) 2 3 4
  2. Identification of a homozygous deletion mutation in C16orf57 in a family with Clericuzio-type poikiloderma with neutropenia. (PMID: 20503306) Tanaka A. … McGrath J. (Am. J. Med. Genet. A 2010) 2 3 4
  3. C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification. (PMID: 22899009) Mroczek S. … Dziembowski A. (Genes Dev. 2012) 2 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for USB1 Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate USB1
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for USB1
    • Block miRNA regulation of USB1 using miScript Target Protectors

    Sources for USB1 Gene

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