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Aliases for USB1 Gene

Aliases for USB1 Gene

  • U6 SnRNA Biogenesis Phosphodiesterase 1 2 3
  • U6 SnRNA Biogenesis 1 2 3 5
  • Mutated In Poikiloderma With Neutropenia Protein 1 2 3
  • HVSL Motif Containing 1 2 3
  • U Six Biogenesis 1 2 3
  • C16orf57 3 4
  • HUsb1 3 4
  • Chromosome 16 Open Reading Frame 57 2
  • Putative U6 SnRNA Phosphodiesterase 3
  • Poikiloderma With Neutropenia 2
  • UPF0406 Protein C16orf57 3
  • EC 3.1.4.- 4
  • HVSL1 3
  • Mpn1 3
  • PN 3

External Ids for USB1 Gene

Previous HGNC Symbols for USB1 Gene

  • C16orf57

Previous GeneCards Identifiers for USB1 Gene

  • GC16P058033

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 Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with USB1 include Poikiloderma With Neutropenia and Dyskeratosis Congenita. GO annotations related to this gene include nuclease activity and 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

Regulatory Elements for USB1 Gene

Enhancers for USB1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around USB1 on UCSC Golden Path with GeneCards custom track

Promoters for USB1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USB1 on UCSC Golden Path with GeneCards custom track

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

Genes around USB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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 & Families for USB1 Gene

Protein Domains for USB1 Gene


Suggested Antigen Peptide Sequences for USB1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the 2H phosphoesterase superfamily. USB1 family.
  • Belongs to the 2H phosphoesterase superfamily. USB1 family.
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

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

Human Phenotype Ontology for USB1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for USB1 Gene

Localization for USB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USB1 Gene

Subcellular locations from

Jensen Localization Image for USB1 Gene COMPARTMENTS Subcellular localization image for USB1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for USB1 Gene

Pathways & Interactions 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:0008380 RNA splicing IMP 22899009
GO:0034477 U6 snRNA 3-end processing IEA,IMP 22899009
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
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 and SIGNOR curated interactions for USB1 Gene

Drugs & Compounds for USB1 Gene

No Compound Related Data Available

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 (x9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with USB1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for USB1 Gene

Orthologs for USB1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for USB1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia USB1 35
  • 86.92 (n)
  • 83.77 (a)
USB1 36
  • 84 (a)
(Canis familiaris)
Mammalia USB1 35
  • 86.11 (n)
  • 83.33 (a)
USB1 36
  • 59 (a)
(Mus musculus)
Mammalia Usb1 35
  • 83.4 (n)
  • 81.13 (a)
Usb1 16
Usb1 36
  • 81 (a)
(Pan troglodytes)
Mammalia USB1 35
  • 99.5 (n)
  • 98.49 (a)
C16ORF57 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Usb1 35
  • 84.15 (n)
  • 83.4 (a)
(Monodelphis domestica)
Mammalia USB1 36
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia USB1 36
  • 71 (a)
(Gallus gallus)
Aves C11H16ORF57 35
  • 71.55 (n)
  • 65.97 (a)
USB1 36
  • 69 (a)
(Anolis carolinensis)
Reptilia USB1 36
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia usb1 35
  • 61.62 (n)
  • 55.41 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC52944 35
(Danio rerio)
Actinopterygii usb1 35
  • 58.93 (n)
  • 50.45 (a)
usb1 36
  • 46 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2636 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002220 35
  • 49.43 (n)
  • 38.54 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG16790 35
  • 51.37 (n)
  • 42.78 (a)
CG16790 36
  • 36 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G51170 35
  • 45.49 (n)
  • 39.06 (a)
(Oryza sativa)
Liliopsida Os02g0651000 35
  • 40.79 (n)
  • 32.17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 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
rs16959641 - 58,020,195(+) CTGAG(C/G)AAGTC reference, missense
rs35025252 - 58,010,007(+) GGTAA(A/G)GATGA nc-transcript-variant, reference, missense
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

Variation tolerance for USB1 Gene

Residual Variation Intolerance Score: 69.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.16; 61.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USB1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for USB1 Gene

Disorders for USB1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for USB1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
poikiloderma with neutropenia
  • clericuzio type poikiloderma with neutropenia
dyskeratosis congenita
  • revesz syndrome
rothmund-thomson syndrome
  • erythrokeratodermia variabilis
  • leukopenia
  • pathologic calcification
- elite association - COSMIC cancer census association via MalaCards
Search USB1 in MalaCards View complete list of genes associated with diseases


  • 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.

Relevant External Links for USB1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with USB1: view

No data available for Genatlas for USB1 Gene

Publications for USB1 Gene

  1. 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 67
  2. Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA. (PMID: 23022480) Shchepachev V. … Azzalin C.M. (Cell Rep 2012) 2 3
  3. 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. 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
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for USB1 Gene

Sources for USB1 Gene