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Q9BQ65 (USB1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U6 snRNA phosphodiesterase

Short name=hUsb1
EC=3.1.4.-
Gene names
Name:USB1
Synonyms:C16orf57
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length265 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.6 Ref.7

Subcellular location

Nucleus Ref.6.

Involvement in disease

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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.4 Ref.5

Sequence similarities

Belongs to the USB1 family.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   Molecular functionHydrolase
Nuclease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA phosphodiester bond hydrolysis, exonucleolytic

Inferred from direct assay Ref.7. Source: GOC

RNA splicing

Inferred from mutant phenotype Ref.6. Source: UniProtKB

U6 snRNA 3'-end processing

Inferred from mutant phenotype Ref.6. Source: UniProtKB

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.6. Source: UniProtKB

   Molecular_function3'-5'-exoribonuclease activity

Inferred from direct assay Ref.7. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9BQ65-1)

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.
Isoform 2 (identifier: Q9BQ65-2)

The sequence of this isoform differs from the canonical sequence as follows:
     150-167: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9BQ65-3)

The sequence of this isoform differs from the canonical sequence as follows:
     150-265: RFFFTANQVK...GNKFFSMPLK → SPHPGPHCLI...LRQEPGSQTR
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 265265U6 snRNA phosphodiesterase HAMAP-Rule MF_03040
PRO_0000274391

Sites

Active site1201Proton donor/acceptor Probable
Active site2081Proton donor/acceptor Probable

Natural variations

Alternative sequence150 – 265116RFFFT…SMPLK → SPHPGPHCLIGTKDAPVTQE IPKDLGALRQEPGSQTR in isoform 3.
VSP_042936
Alternative sequence150 – 16718Missing in isoform 2.
VSP_042878
Natural variant1151R → K.
Corresponds to variant rs35025252 [ dbSNP | Ensembl ].
VAR_053822
Natural variant2501Q → E.
Corresponds to variant rs16959641 [ dbSNP | Ensembl ].
VAR_030277

Experimental info

Mutagenesis1201H → A: Abolishes exoribonuclease activity. Ref.7
Mutagenesis2081H → A: Abolishes exoribonuclease activity. No rescue of the molecular phenotype caused by USB1 depletion. Ref.6 Ref.7
Sequence conflict891Y → C in AAH10099. Ref.3
Sequence conflict2091L → P in BAB14469. Ref.1

Secondary structure

............................. 265
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: 75D8BF51DF8D353D

FASTA26530,268
        10         20         30         40         50         60 
MSAAPLVGYS SSGSEDESED GMRTRPGDGS HRRGQSPLPR QRFPVPDSVL NMFPGTEEGP 

        70         80         90        100        110        120 
EDDSTKHGGR VRTFPHERGN WATHVYVPYE AKEEFLDLLD VLLPHAQTYV PRLVRMKVFH 

       130        140        150        160        170        180 
LSLSQSVVLR HHWILPFVQA LKARMTSFHR FFFTANQVKI YTNQEKTRTF IGLEVTSGHA 

       190        200        210        220        230        240 
QFLDLVSEVD RVMEEFNLTT FYQDPSFHLS LAWCVGDARL QLEGQCLQEL QAIVDGFEDA 

       250        260 
EVLLRVHTEQ VRCKSGNKFF SMPLK 

« Hide

Isoform 2 [UniParc].

Checksum: E2A5B443D8385DF4
Show »

FASTA24728,051
Isoform 3 [UniParc].

Checksum: B319207B0717EF30
Show »

FASTA18620,802

References

« Hide 'large scale' references
[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
Tissue: Synovium and Thymus.
[2]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Kidney, Pancreas, Placenta, Skin and Uterus.
[4]"Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene."
Volpi L., Roversi G., Colombo E.A., Leijsten N., Concolino D., Calabria A., Mencarelli M.A., Fimiani M., Macciardi F., Pfundt R., Schoenmakers E.F., Larizza L.
Am. J. Hum. Genet. 86:72-76(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN PN.
[5]"Identification of a homozygous deletion mutation in C16orf57 in a family with Clericuzio-type poikiloderma with neutropenia."
Tanaka A., Morice-Picard F., Lacombe D., Nagy N., Hide M., Taieb A., McGrath J.
Am. J. Med. Genet. A 152:1347-1348(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN PN.
[6]"C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification."
Mroczek S., Krwawicz J., Kutner J., Lazniewski M., Kucinski I., Ginalski K., Dziembowski A.
Genes Dev. 26:1911-1925(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, FUNCTION, MUTAGENESIS OF HIS-208.
[7]"Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia."
Hilcenko C., Simpson P.J., Finch A.J., Bowler F.R., Churcher M.J., Jin L., Packman L.C., Shlien A., Campbell P., Kirwan M., Dokal I., Warren A.J.
Blood 121:1028-1038(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS) OF 73-265, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE, MUTAGENESIS OF HIS-120 AND HIS-208.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS10791.1. [Q9BQ65-1]
CCDS55997.1. [Q9BQ65-3]
CCDS55998.1. [Q9BQ65-2]
RefSeqNP_001182231.1. NM_001195302.1. [Q9BQ65-2]
NP_001191840.1. NM_001204911.1. [Q9BQ65-3]
NP_078874.2. NM_024598.3. [Q9BQ65-1]
UniGeneHs.408702.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4H7WX-ray1.10A73-265[»]
ProteinModelPortalQ9BQ65.
SMRQ9BQ65. Positions 79-265.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122778. 7 interactions.
IntActQ9BQ65. 2 interactions.
MINTMINT-1184765.
STRING9606.ENSP00000219281.

PTM databases

PhosphoSiteQ9BQ65.

Polymorphism databases

DMDM74732815.

Proteomic databases

MaxQBQ9BQ65.
PaxDbQ9BQ65.
PRIDEQ9BQ65.

Protocols and materials databases

DNASU79650.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000219281; ENSP00000219281; ENSG00000103005. [Q9BQ65-1]
ENST00000423271; ENSP00000409792; ENSG00000103005. [Q9BQ65-3]
ENST00000539737; ENSP00000446143; ENSG00000103005. [Q9BQ65-2]
GeneID79650.
KEGGhsa:79650.
UCSCuc002emz.3. human. [Q9BQ65-1]
uc010via.2. human. [Q9BQ65-3]
uc010vib.2. human. [Q9BQ65-2]

Organism-specific databases

CTD79650.
GeneCardsGC16P058033.
H-InvDBHIX0019615.
HGNCHGNC:25792. USB1.
HPAHPA041791.
MIM604173. phenotype.
613276. gene.
neXtProtNX_Q9BQ65.
Orphanet1775. Dyskeratosis congenita.
221046. Poikiloderma with neutropenia.
PharmGKBPA143485394.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG251744.
HOGENOMHOG000213585.
HOVERGENHBG081315.
InParanoidQ9BQ65.
OMAHHWIQPF.
PhylomeDBQ9BQ65.
TreeFamTF324364.

Gene expression databases

ArrayExpressQ9BQ65.
BgeeQ9BQ65.
CleanExHS_C16orf57.
GenevestigatorQ9BQ65.

Family and domain databases

HAMAPMF_03040. USB1.
InterProIPR027521. Usb1.
[Graphical view]
PANTHERPTHR13522. PTHR13522. 1 hit.
PfamPF09749. HVSL. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSC16orf57. human.
GenomeRNAi79650.
NextBio68808.
SOURCESearch...

Entry information

Entry nameUSB1_HUMAN
AccessionPrimary (citable) accession number: Q9BQ65
Secondary accession number(s): B4DWE3 expand/collapse secondary AC list , B4DZW5, Q96FZ9, Q9H8X8
Entry history
Integrated into UniProtKB/Swiss-Prot: February 6, 2007
Last sequence update: June 1, 2001
Last modified: July 9, 2014
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM