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, exp... See more...

Aliases for USB1 Gene

Aliases for USB1 Gene

  • U6 SnRNA Biogenesis Phosphodiesterase 1 2 3 5
  • Mutated In Poikiloderma With Neutropenia Protein 1 2 3
  • U6 SnRNA Phosphodiesterase 3 4
  • HVSL Motif Containing 1 2 3
  • U6 SnRNA Biogenesis 1 2 3
  • U Six Biogenesis 1 2 3
  • C16orf57 3 4
  • HUsb1 3 4
  • Putative U6 SnRNA Phosphodiesterase 3
  • Chromosome 16 Open Reading Frame 57 2
  • 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. Gene Ontology (GO) annotations related to this gene include nuclease activity and 3'-5'-exoribonuclease activity.

UniProtKB/Swiss-Prot Summary 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.

Additional gene information for USB1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USB1 Gene

Genomics for USB1 Gene

GeneHancer (GH) Regulatory Elements for USB1 Gene

Promoters and enhancers for USB1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J057998 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.8 800 4.5 ZBTB40 CTCF SIN3A NRF1 USF1 POLR2G SP1 NCOR1 GTF2E2 PHF8 NONHSAG019587.2 ZNF319 USB1 TEPP
GH16J057482 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 6.5 -514.7 -514725 5.3 ZBTB40 EP300 NRF1 POLR2G NCOR1 ZFX ZIC2 POLR2A KDM6A ZBTB10 DOK4 CIAPIN1 COQ9 LOC105371286 POLR2C CX3CL1 CCL22 USB1 lnc-CIAPIN1-2
GH16J057666 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 1.5 -331.3 -331328 3.6 EP300 CTCF POLR2G GTF2E2 KDM6A ZNF263 AFF1 TARDBP ZBTB7A CTBP1 ADGRG3 DRC7 ZNF319 CCDC102A CNOT1 RSPRY1 ENSG00000261114 ENSG00000260467 PSME3IP1 USB1
GH16J058020 Enhancer 1.1 ENCODE dbSUPER 0.4 +21.3 21269 1.1 CTCF BCLAF1 NONO ZBTB5 FOXA1 REST DNMT1 ZBTB25 MYC RAD21 CNOT1 POLR2C RSPRY1 TEPP CCDC102A CNGB1 CSNK2A2 MMP15 NONHSAG019587.2 USB1
GH16J058005 Enhancer 0.7 Ensembl 0.4 +5.8 5755 1 CTCF REST RFX1 TRIM22 CTBP1 SMC3 KAT7 FOS MEF2B NBN TEPP NONHSAG019587.2 USB1 MMP15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USB1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USB1

Genomic Locations for USB1 Gene

Genomic Locations for USB1 Gene
chr16:57,999,546-58,021,623
(GRCh38/hg38)
Size:
22,078 bases
Orientation:
Plus strand
chr16:58,033,450-58,055,527
(GRCh37/hg19)
Size:
22,078 bases
Orientation:
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:
    Q9BQ65-USB1_HUMAN
    Recommended name:
    U6 snRNA phosphodiesterase
    Protein Accession:
    Q9BQ65
    Secondary Accessions:
    • B4DWE3
    • B4DZW5
    • Q96FZ9
    • Q9H8X8

    Protein attributes for USB1 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for USB1 Gene

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

Gene Families for USB1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for USB1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for USB1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59088 (B4DWE3_HUMAN)
  • cDNA FLJ60009 (B4DZW5_HUMAN)
  • UPF0406 protein C16orf57 (CP057_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BQ65

UniProtKB/Swiss-Prot:

USB1_HUMAN :
  • Belongs to the 2H phosphoesterase superfamily. USB1 family.
Family:
  • Belongs to the 2H phosphoesterase superfamily. USB1 family.
genes like me logo Genes that share domains with USB1: view

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 IEA --
GO:0016787 hydrolase activity IEA --
GO:1990838 poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends IEA --
genes like me logo Genes that share ontologies with USB1: view
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USB1

Clone Products

No data available for Phenotypes From GWAS Catalog , 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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USB1 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for USB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 22899009
GO:0005654 nucleoplasm IDA --
GO:0045171 intercellular bridge IDA --
genes like me logo Genes that share ontologies with USB1: view

Pathways & Interactions for USB1 Gene

PathCards logo

SuperPathways for USB1 Gene

No Data Available

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 IMP,IEA 22899009
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic IEA --
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

mRNA/cDNA for USB1 Gene

5 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USB1

Clone Products

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: - - - - - - - -
SP9:
SP10:

Relevant External Links for USB1 Gene

GeneLoc Exon Structure for
USB1

Expression for USB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for USB1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USB1

SOURCE GeneReport for Unigene cluster for USB1 Gene:

Hs.408702

Evidence on tissue expression from TISSUES for USB1 Gene

  • Skin(4.4)
  • Kidney(4.2)
  • Pancreas(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for USB1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lacrimal apparatus
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • pharynx
  • salivary gland
  • scalp
  • skull
  • tooth
Thorax:
  • breast
  • chest wall
  • clavicle
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • rectum
  • testicle
  • urethra
  • urinary bladder
  • uterus
  • vagina
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with USB1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt 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
chimpanzee
(Pan troglodytes)
Mammalia USB1 30
  • 99.5 (n)
C16ORF57 31
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USB1 31 30
  • 86.92 (n)
OneToOne
dog
(Canis familiaris)
Mammalia USB1 31 30
  • 86.11 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usb1 30
  • 84.15 (n)
mouse
(Mus musculus)
Mammalia Usb1 17 31 30
  • 83.4 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia USB1 31
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USB1 31
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves C11H16ORF57 30
  • 71.55 (n)
USB1 31
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USB1 31
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usb1 30
  • 61.62 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC52944 30
zebrafish
(Danio rerio)
Actinopterygii usb1 31 30
  • 58.93 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2636 30
fruit fly
(Drosophila melanogaster)
Insecta CG16790 31 30
  • 51.37 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002220 30
  • 49.43 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G51170 30
  • 45.49 (n)
rice
(Oryza sativa)
Liliopsida Os02g0651000 30
  • 40.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 26 (a)
OneToOne
Species where no ortholog for USB1 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for USB1 (if available)
TreeFam:
Gene Tree for USB1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USB1: view image

Paralogs for USB1 Gene

No data available for Paralogs for USB1 Gene

Variants for USB1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USB1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
714808 Benign: not provided 58,009,975(+) C/T SYNONYMOUS_VARIANT
727659 Likely Benign: not provided 58,014,336(+) C/G INTRON_VARIANT
733957 Likely Benign: not provided 58,010,121(+) T/G INTRON_VARIANT
737166 Likely Benign: not provided 58,009,990(+) T/C SYNONYMOUS_VARIANT
748273 Likely Benign: not provided 58,001,561(+) G/C SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for USB1 Gene

Structural Variations from Database of Genomic Variants (DGV) for USB1 Gene

Variant ID Type Subtype PubMed ID
dgv525e214 CNV gain 21293372
esv1994917 CNV deletion 18987734
esv2714545 CNV deletion 23290073
esv3638716 CNV loss 21293372
nsv1063386 CNV gain 25217958
nsv1816 CNV deletion 18451855
nsv572759 CNV loss 21841781
nsv827685 CNV gain 20364138

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)

Additional Variant Information for USB1 Gene

Human Gene Mutation Database (HGMD)
USB1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USB1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USB1 Gene

Disorders for USB1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
poikiloderma with neutropenia
  • pn
dyskeratosis congenita
  • zinsser-cole-engman syndrome
neutropenia
  • leukopenia
rothmund-thomson syndrome, type 2
  • rts2
revesz syndrome
  • dyskeratosis congenita, autosomal dominant 5; dkca5
- elite association - COSMIC cancer census association via MalaCards
Search USB1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

USB1_HUMAN
  • 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.

Additional Disease Information for USB1

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 & development 2012) 2 3 4 54
  2. Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. (PMID: 20004881) Volpi L … Larizza L (American journal of human genetics 2010) 2 3 4 54
  3. Identification of a homozygous deletion mutation in C16orf57 in a family with Clericuzio-type poikiloderma with neutropenia. (PMID: 20503306) Tanaka A … McGrath J (American journal of medical genetics. Part A 2010) 2 3 4 54
  4. Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia. (PMID: 23190533) Hilcenko C … Warren AJ (Blood 2013) 3 4 54
  5. 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 CM (Cell reports 2012) 2 3 54

Products for USB1 Gene

Sources for USB1 Gene