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Q9BQ65

- USB1_HUMAN

UniProt

Q9BQ65 - USB1_HUMAN

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Protein

U6 snRNA phosphodiesterase

Gene

USB1

Organism
Homo sapiens (Human)
Status
Reviewed - 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.2 PublicationsUniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei120 – 1201Proton donor/acceptor1 Publication
Active sitei208 – 2081Proton donor/acceptor1 Publication

GO - Molecular functioni

  1. 3'-5'-exoribonuclease activity Source: UniProtKB

GO - Biological processi

  1. mRNA processing Source: UniProtKB-KW
  2. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
  3. RNA splicing Source: UniProtKB
  4. U6 snRNA 3'-end processing Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, mRNA splicing

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
ProteomesiUP000005640: Chromosome 16

Organism-specific databases

HGNCiHGNC:25792. USB1.

Subcellular locationi

Nucleus 1 PublicationUniRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

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.2 Publications
Note: The disease is caused by mutations affecting the gene represented in this entry.

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi120 – 1201H → A: Abolishes exoribonuclease activity. 1 Publication
Mutagenesisi208 – 2081H → A: Abolishes exoribonuclease activity. No rescue of the molecular phenotype caused by USB1 depletion. 2 Publications

Organism-specific databases

MIMi604173. phenotype.
Orphaneti1775. Dyskeratosis congenita.
221046. Poikiloderma with neutropenia.
PharmGKBiPA143485394.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 265265U6 snRNA phosphodiesterasePRO_0000274391Add
BLAST

Proteomic databases

MaxQBiQ9BQ65.
PaxDbiQ9BQ65.
PRIDEiQ9BQ65.

PTM databases

PhosphoSiteiQ9BQ65.

Expressioni

Gene expression databases

BgeeiQ9BQ65.
CleanExiHS_C16orf57.
ExpressionAtlasiQ9BQ65. baseline and differential.
GenevestigatoriQ9BQ65.

Organism-specific databases

HPAiHPA041791.

Interactioni

Protein-protein interaction databases

BioGridi122778. 27 interactions.
IntActiQ9BQ65. 2 interactions.
MINTiMINT-1184765.
STRINGi9606.ENSP00000219281.

Structurei

Secondary structure

1
265
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi80 – 8910
Helixi93 – 10715
Beta strandi117 – 1226
Beta strandi127 – 1304
Helixi131 – 1333
Helixi134 – 14512
Beta strandi155 – 1628
Beta strandi166 – 17510
Helixi179 – 19517
Beta strandi208 – 2169
Helixi219 – 2224
Helixi225 – 23511
Helixi241 – 2444
Beta strandi250 – 2556
Beta strandi258 – 2636

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H7WX-ray1.10A73-265[»]
ProteinModelPortaliQ9BQ65.
SMRiQ9BQ65. Positions 79-265.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the USB1 family.UniRule annotation

Phylogenomic databases

eggNOGiNOG251744.
GeneTreeiENSGT00390000004596.
HOGENOMiHOG000213585.
HOVERGENiHBG081315.
InParanoidiQ9BQ65.
OMAiHHWIQPF.
PhylomeDBiQ9BQ65.
TreeFamiTF324364.

Family and domain databases

HAMAPiMF_03040. USB1.
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. Align

Isoform 1 (identifier: Q9BQ65) [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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti89 – 891Y → C in AAH10099. (PubMed:15489334)Curated
Sequence conflicti209 – 2091L → P in BAB14469. (PubMed:14702039)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti115 – 1151R → K.
Corresponds to variant rs35025252 [ dbSNP | Ensembl ].
VAR_053822
Natural varianti250 – 2501Q → E.
Corresponds to variant rs16959641 [ dbSNP | Ensembl ].
VAR_030277

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei150 – 265116RFFFT…SMPLK → SPHPGPHCLIGTKDAPVTQE IPKDLGALRQEPGSQTR in isoform 3. 1 PublicationVSP_042936Add
BLAST
Alternative sequencei150 – 16718Missing in isoform 2. 1 PublicationVSP_042878Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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_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.3. human. [Q9BQ65-1]
uc010via.2. human. [Q9BQ65-3]
uc010vib.2. human. [Q9BQ65-2]

Polymorphism databases

DMDMi74732815.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS10791.1. [Q9BQ65-1 ]
CCDS55997.1. [Q9BQ65-3 ]
CCDS55998.1. [Q9BQ65-2 ]
RefSeqi NP_001182231.1. NM_001195302.1. [Q9BQ65-2 ]
NP_001191840.1. NM_001204911.1. [Q9BQ65-3 ]
NP_078874.2. NM_024598.3. [Q9BQ65-1 ]
UniGenei Hs.408702.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4H7W X-ray 1.10 A 73-265 [» ]
ProteinModelPortali Q9BQ65.
SMRi Q9BQ65. Positions 79-265.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 122778. 27 interactions.
IntActi Q9BQ65. 2 interactions.
MINTi MINT-1184765.
STRINGi 9606.ENSP00000219281.

PTM databases

PhosphoSitei Q9BQ65.

Polymorphism databases

DMDMi 74732815.

Proteomic databases

MaxQBi Q9BQ65.
PaxDbi Q9BQ65.
PRIDEi Q9BQ65.

Protocols and materials databases

DNASUi 79650.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000219281 ; ENSP00000219281 ; ENSG00000103005 . [Q9BQ65-1 ]
ENST00000423271 ; ENSP00000409792 ; ENSG00000103005 . [Q9BQ65-3 ]
ENST00000539737 ; ENSP00000446143 ; ENSG00000103005 . [Q9BQ65-2 ]
GeneIDi 79650.
KEGGi hsa:79650.
UCSCi uc002emz.3. human. [Q9BQ65-1 ]
uc010via.2. human. [Q9BQ65-3 ]
uc010vib.2. human. [Q9BQ65-2 ]

Organism-specific databases

CTDi 79650.
GeneCardsi GC16P058033.
H-InvDB HIX0019615.
HGNCi HGNC:25792. USB1.
HPAi HPA041791.
MIMi 604173. phenotype.
613276. gene.
neXtProti NX_Q9BQ65.
Orphaneti 1775. Dyskeratosis congenita.
221046. Poikiloderma with neutropenia.
PharmGKBi PA143485394.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG251744.
GeneTreei ENSGT00390000004596.
HOGENOMi HOG000213585.
HOVERGENi HBG081315.
InParanoidi Q9BQ65.
OMAi HHWIQPF.
PhylomeDBi Q9BQ65.
TreeFami TF324364.

Miscellaneous databases

ChiTaRSi C16orf57. human.
GenomeRNAii 79650.
NextBioi 68808.
SOURCEi Search...

Gene expression databases

Bgeei Q9BQ65.
CleanExi HS_C16orf57.
ExpressionAtlasi Q9BQ65. baseline and differential.
Genevestigatori Q9BQ65.

Family and domain databases

HAMAPi MF_03040. USB1.
InterProi IPR027521. Usb1.
[Graphical view ]
PANTHERi PTHR13522. PTHR13522. 1 hit.
Pfami PF09749. HVSL. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
    , 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.

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: October 29, 2014
This is version 94 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

External Data

Dasty 3