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Protein

U6 snRNA phosphodiesterase

Gene

USB1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei120Proton donor/acceptor1 Publication1
Active sitei208Proton donor/acceptor1 Publication1

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • RNA splicing Source: UniProtKB
  • U6 snRNA 3'-end processing Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciZFISH:ENSG00000103005-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA phosphodiesteraseUniRule annotation (EC:3.1.4.-UniRule annotation)
Short name:
hUsb1
Gene namesi
Name:USB1UniRule annotation
Synonyms:C16orf57
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:25792. USB1.

Subcellular locationi

  • Nucleus UniRule annotation1 Publication

GO - Cellular componenti

  • intercellular bridge Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Poikiloderma with neutropenia (PN)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:604173

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi120H → A: Abolishes exoribonuclease activity. 1 Publication1
Mutagenesisi208H → A: Abolishes exoribonuclease activity. No rescue of the molecular phenotype caused by USB1 depletion. 2 Publications1

Organism-specific databases

DisGeNETi79650.
MalaCardsiUSB1.
MIMi604173. phenotype.
OpenTargetsiENSG00000103005.
Orphaneti1775. Dyskeratosis congenita.
221046. Poikiloderma with neutropenia.
PharmGKBiPA143485394.

Polymorphism and mutation databases

BioMutaiUSB1.
DMDMi74732815.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002743911 – 265U6 snRNA phosphodiesteraseAdd BLAST265

Proteomic databases

EPDiQ9BQ65.
MaxQBiQ9BQ65.
PaxDbiQ9BQ65.
PeptideAtlasiQ9BQ65.
PRIDEiQ9BQ65.

PTM databases

iPTMnetiQ9BQ65.
PhosphoSitePlusiQ9BQ65.

Expressioni

Gene expression databases

BgeeiENSG00000103005.
CleanExiHS_C16orf57.
ExpressionAtlasiQ9BQ65. baseline and differential.
GenevisibleiQ9BQ65. HS.

Organism-specific databases

HPAiHPA041791.
HPA059854.

Interactioni

Protein-protein interaction databases

BioGridi122778. 31 interactors.
IntActiQ9BQ65. 2 interactors.
MINTiMINT-1184765.
STRINGi9606.ENSP00000219281.

Structurei

Secondary structure

1265
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi80 – 89Combined sources10
Helixi93 – 107Combined sources15
Beta strandi117 – 122Combined sources6
Beta strandi127 – 130Combined sources4
Helixi131 – 133Combined sources3
Helixi134 – 145Combined sources12
Beta strandi155 – 162Combined sources8
Beta strandi166 – 175Combined sources10
Helixi179 – 195Combined sources17
Beta strandi208 – 216Combined sources9
Helixi219 – 222Combined sources4
Helixi225 – 235Combined sources11
Helixi241 – 244Combined sources4
Beta strandi250 – 255Combined sources6
Beta strandi258 – 263Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4H7WX-ray1.10A73-265[»]
ProteinModelPortaliQ9BQ65.
SMRiQ9BQ65.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the 2H phosphoesterase superfamily. USB1 family.UniRule annotation

Phylogenomic databases

eggNOGiKOG3102. Eukaryota.
ENOG4111KT5. LUCA.
GeneTreeiENSGT00390000004596.
HOGENOMiHOG000047515.
HOVERGENiHBG081315.
InParanoidiQ9BQ65.
OMAiRCRTGNK.
OrthoDBiEOG091G0HOU.
PhylomeDBiQ9BQ65.
TreeFamiTF324364.

Family and domain databases

HAMAPiMF_03040. USB1. 1 hit.
InterProiIPR027521. Usb1.
[Graphical view]
PANTHERiPTHR13522. PTHR13522. 1 hit.
PfamiPF09749. HVSL. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BQ65-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSAAPLVGYS SSGSEDESED GMRTRPGDGS HRRGQSPLPR QRFPVPDSVL
60 70 80 90 100
NMFPGTEEGP EDDSTKHGGR VRTFPHERGN WATHVYVPYE AKEEFLDLLD
110 120 130 140 150
VLLPHAQTYV PRLVRMKVFH LSLSQSVVLR HHWILPFVQA LKARMTSFHR
160 170 180 190 200
FFFTANQVKI YTNQEKTRTF IGLEVTSGHA QFLDLVSEVD RVMEEFNLTT
210 220 230 240 250
FYQDPSFHLS LAWCVGDARL QLEGQCLQEL QAIVDGFEDA EVLLRVHTEQ
260
VRCKSGNKFF SMPLK
Length:265
Mass (Da):30,268
Last modified:June 1, 2001 - v1
Checksum:i75D8BF51DF8D353D
GO
Isoform 2 (identifier: Q9BQ65-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     150-167: Missing.

Note: No experimental confirmation available.
Show »
Length:247
Mass (Da):28,051
Checksum:iE2A5B443D8385DF4
GO
Isoform 3 (identifier: Q9BQ65-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     150-265: RFFFTANQVK...GNKFFSMPLK → SPHPGPHCLI...LRQEPGSQTR

Note: No experimental confirmation available.
Show »
Length:186
Mass (Da):20,802
Checksum:iB319207B0717EF30
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti89Y → C in AAH10099 (PubMed:15489334).Curated1
Sequence conflicti209L → P in BAB14469 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_053822115R → K.Corresponds to variant rs35025252dbSNPEnsembl.1
Natural variantiVAR_030277250Q → E.Corresponds to variant rs16959641dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_042936150 – 265RFFFT…SMPLK → SPHPGPHCLIGTKDAPVTQE IPKDLGALRQEPGSQTR in isoform 3. 1 PublicationAdd BLAST116
Alternative sequenceiVSP_042878150 – 167Missing in isoform 2. 1 PublicationAdd BLAST18

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK023216 mRNA. Translation: BAB14469.1.
AK301494 mRNA. Translation: BAG63005.1.
AK303121 mRNA. Translation: BAG64227.1.
AC010543 Genomic DNA. No translation available.
AC012182 Genomic DNA. No translation available.
BC004415 mRNA. Translation: AAH04415.1.
BC006291 mRNA. Translation: AAH06291.1.
BC007774 mRNA. Translation: AAH07774.1.
BC010099 mRNA. Translation: AAH10099.1.
BC021554 mRNA. Translation: AAH21554.1.
CCDSiCCDS10791.1. [Q9BQ65-1]
CCDS55997.1. [Q9BQ65-3]
CCDS55998.1. [Q9BQ65-2]
RefSeqiNP_001182231.1. NM_001195302.1. [Q9BQ65-2]
NP_001191840.1. NM_001204911.1. [Q9BQ65-3]
NP_001317497.1. NM_001330568.1.
NP_078874.2. NM_024598.3. [Q9BQ65-1]
UniGeneiHs.408702.

Genome annotation databases

EnsembliENST00000219281; ENSP00000219281; ENSG00000103005. [Q9BQ65-1]
ENST00000423271; ENSP00000409792; ENSG00000103005. [Q9BQ65-3]
ENST00000539737; ENSP00000446143; ENSG00000103005. [Q9BQ65-2]
GeneIDi79650.
KEGGihsa:79650.
UCSCiuc002emz.4. human. [Q9BQ65-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK023216 mRNA. Translation: BAB14469.1.
AK301494 mRNA. Translation: BAG63005.1.
AK303121 mRNA. Translation: BAG64227.1.
AC010543 Genomic DNA. No translation available.
AC012182 Genomic DNA. No translation available.
BC004415 mRNA. Translation: AAH04415.1.
BC006291 mRNA. Translation: AAH06291.1.
BC007774 mRNA. Translation: AAH07774.1.
BC010099 mRNA. Translation: AAH10099.1.
BC021554 mRNA. Translation: AAH21554.1.
CCDSiCCDS10791.1. [Q9BQ65-1]
CCDS55997.1. [Q9BQ65-3]
CCDS55998.1. [Q9BQ65-2]
RefSeqiNP_001182231.1. NM_001195302.1. [Q9BQ65-2]
NP_001191840.1. NM_001204911.1. [Q9BQ65-3]
NP_001317497.1. NM_001330568.1.
NP_078874.2. NM_024598.3. [Q9BQ65-1]
UniGeneiHs.408702.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4H7WX-ray1.10A73-265[»]
ProteinModelPortaliQ9BQ65.
SMRiQ9BQ65.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122778. 31 interactors.
IntActiQ9BQ65. 2 interactors.
MINTiMINT-1184765.
STRINGi9606.ENSP00000219281.

PTM databases

iPTMnetiQ9BQ65.
PhosphoSitePlusiQ9BQ65.

Polymorphism and mutation databases

BioMutaiUSB1.
DMDMi74732815.

Proteomic databases

EPDiQ9BQ65.
MaxQBiQ9BQ65.
PaxDbiQ9BQ65.
PeptideAtlasiQ9BQ65.
PRIDEiQ9BQ65.

Protocols and materials databases

DNASUi79650.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000219281; ENSP00000219281; ENSG00000103005. [Q9BQ65-1]
ENST00000423271; ENSP00000409792; ENSG00000103005. [Q9BQ65-3]
ENST00000539737; ENSP00000446143; ENSG00000103005. [Q9BQ65-2]
GeneIDi79650.
KEGGihsa:79650.
UCSCiuc002emz.4. human. [Q9BQ65-1]

Organism-specific databases

CTDi79650.
DisGeNETi79650.
GeneCardsiUSB1.
H-InvDBHIX0019615.
HGNCiHGNC:25792. USB1.
HPAiHPA041791.
HPA059854.
MalaCardsiUSB1.
MIMi604173. phenotype.
613276. gene.
neXtProtiNX_Q9BQ65.
OpenTargetsiENSG00000103005.
Orphaneti1775. Dyskeratosis congenita.
221046. Poikiloderma with neutropenia.
PharmGKBiPA143485394.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3102. Eukaryota.
ENOG4111KT5. LUCA.
GeneTreeiENSGT00390000004596.
HOGENOMiHOG000047515.
HOVERGENiHBG081315.
InParanoidiQ9BQ65.
OMAiRCRTGNK.
OrthoDBiEOG091G0HOU.
PhylomeDBiQ9BQ65.
TreeFamiTF324364.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000103005-MONOMER.

Miscellaneous databases

GenomeRNAii79650.
PROiQ9BQ65.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000103005.
CleanExiHS_C16orf57.
ExpressionAtlasiQ9BQ65. baseline and differential.
GenevisibleiQ9BQ65. HS.

Family and domain databases

HAMAPiMF_03040. USB1. 1 hit.
InterProiIPR027521. Usb1.
[Graphical view]
PANTHERiPTHR13522. PTHR13522. 1 hit.
PfamiPF09749. HVSL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUSB1_HUMAN
AccessioniPrimary (citable) accession number: Q9BQ65
Secondary accession number(s): B4DWE3
, B4DZW5, Q96FZ9, Q9H8X8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 6, 2007
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families
  7. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.