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Q53GS9 (SNUT2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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:
U4/U6.U5 tri-snRNP-associated protein 2
Alternative name(s):
Inactive ubiquitin-specific peptidase 39
SAD1 homolog
U4/U6.U5 tri-snRNP-associated 65 kDa protein
Short name=65K
Gene names
Name:USP39
ORF Names:CGI-21, HSPC332, PRO2855
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length565 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the spliceosome. Regulates AURKB mRNA levels, and thereby plays a role in cytokinesis and in the spindle checkpoint. Does not have ubiquitin-specific peptidase activity, but could be a competitor of ubiquitin C-terminal hydrolases (UCHs). Ref.1 Ref.12

Subunit structure

Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39. Ref.11

Subcellular location

Nucleus Ref.1.

Sequence similarities

Belongs to the peptidase C19 family.

Contains 1 UBP-type zinc finger.

Contains 1 USP domain.

Sequence caution

The sequence AAD27730.1 differs from that shown. Reason: Frameshift at several positions.

The sequence AAG35521.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q53GS9-1)

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: Q53GS9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-89: MSGRSKRESR...EDSEPEREVR → MLTAVPSHLFS
     113-144: RSVLDFDFEKLCSISLSHINAYACLVCGKYFQ → SFSPFPT
Isoform 3 (identifier: Q53GS9-3)

The sequence of this isoform differs from the canonical sequence as follows:
     477-565: NVDLREYLSE...DNDETNQQGA → GQANGMNYKTSR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 565565U4/U6.U5 tri-snRNP-associated protein 2
PRO_0000223962

Regions

Domain225 – 555331USP
Zinc finger122 – 18362UBP-type
Compositional bias4 – 103100Arg-rich

Amino acid modifications

Modified residue821Phosphoserine Ref.10 Ref.14 Ref.16

Natural variations

Alternative sequence1 – 8989MSGRS…EREVR → MLTAVPSHLFS in isoform 2.
VSP_045167
Alternative sequence113 – 14432RSVLD…GKYFQ → SFSPFPT in isoform 2.
VSP_045168
Alternative sequence477 – 56589NVDLR…NQQGA → GQANGMNYKTSR in isoform 3.
VSP_046822

Experimental info

Sequence conflict131T → I in BAD96572. Ref.4
Sequence conflict1351A → V in BAD96572. Ref.4
Sequence conflict2771F → S in BAG50852. Ref.3
Sequence conflict2801L → P in BAG50852. Ref.3
Sequence conflict2941V → A in BAG50852. Ref.3
Sequence conflict4001L → F in AAK49524. Ref.1
Sequence conflict4561R → I in AAD27730. Ref.2

Sequences

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

Last modified February 21, 2006. Version 2.
Checksum: 8946FD5DCDEFD0B0

FASTA56565,381
        10         20         30         40         50         60 
MSGRSKRESR GSTRGKRESE SRGSSGRVKR ERDREREPEA ASSRGSPVRV KREFEPASAR 

        70         80         90        100        110        120 
EAPASVVPFV RVKREREVDE DSEPEREVRA KNGRVDSEDR RSRHCPYLDT INRSVLDFDF 

       130        140        150        160        170        180 
EKLCSISLSH INAYACLVCG KYFQGRGLKS HAYIHSVQFS HHVFLNLHTL KFYCLPDNYE 

       190        200        210        220        230        240 
IIDSSLEDIT YVLKPTFTKQ QIANLDKQAK LSRAYDGTTY LPGIVGLNNI KANDYANAVL 

       250        260        270        280        290        300 
QALSNVPPLR NYFLEEDNYK NIKRPPGDIM FLLVQRFGEL MRKLWNPRNF KAHVSPHEML 

       310        320        330        340        350        360 
QAVVLCSKKT FQITKQGDGV DFLSWFLNAL HSALGGTKKK KKTIVTDVFQ GSMRIFTKKL 

       370        380        390        400        410        420 
PHPDLPAEEK EQLLHNDEYQ ETMVESTFMY LTLDLPTAPL YKDEKEQLII PQVPLFNILA 

       430        440        450        460        470        480 
KFNGITEKEY KTYKENFLKR FQLTKLPPYL IFCIKRFTKN NFFVEKNPTI VNFPITNVDL 

       490        500        510        520        530        540 
REYLSEEVQA VHKNTTYDLI ANIVHDGKPS EGSYRIHVLH HGTGKWYELQ DLQVTDILPQ 

       550        560 
MITLSEAYIQ IWKRRDNDET NQQGA 

« Hide

Isoform 2 [UniParc].

Checksum: C57BF48DC1B0F9D5
Show »

FASTA46253,510
Isoform 3 [UniParc].

Checksum: 757387284D021074
Show »

FASTA48856,359

References

« Hide 'large scale' references
[1]"The 65 and 110 kDa SR-related proteins of the U4/U6*U5 tri-snRNP are essential for the assembly of mature spliceosomes."
Makarova O.V., Makarov E.M., Luehrmann R.
EMBO J. 20:2553-2563(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION.
[2]"Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics."
Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.
Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]"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: Caudate nucleus and Embryo.
[4]Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Liver.
[5]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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: Skin and Uterus.
[8]"Functional prediction of the coding sequences of 75 new genes deduced by analysis of cDNA clones from human fetal liver."
Zhang C., Yu Y., Zhang S., Wei H., Bi J., Zhou G., Dong C., Zai Y., Xu W., Gao F., Liu M., He F.
Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 104-565.
Tissue: Fetal liver.
[9]"Human partial CDS from CD34+ stem cells."
Ye M., Zhang Q.-H., Zhou J., Shen Y., Wu X.-Y., Guan Z.Q., Wang L., Fan H.-Y., Mao Y.-F., Dai M., Huang Q.-H., Chen S.-J., Chen Z.
Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 305-565.
Tissue: Umbilical cord blood.
[10]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[12]"Usp39 is essential for mitotic spindle checkpoint integrity and controls mRNA-levels of aurora B."
van Leuken R.J., Luna-Vargas M.P., Sixma T.K., Wolthuis R.M., Medema R.H.
Cell Cycle 7:2710-2719(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ABSENCE OF UBIQUITIN-SPECIFIC PEPTIDASE ACTIVITY.
[13]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF353989 mRNA. Translation: AAK49524.1.
AF132955 mRNA. Translation: AAD27730.1. Frameshift.
AK289451 mRNA. Translation: BAF82140.1.
AK001047 mRNA. Translation: BAG50852.1.
AK295257 mRNA. Translation: BAG58246.1.
AK222852 mRNA. Translation: BAD96572.1.
AC012454 Genomic DNA. No translation available.
AC016753 Genomic DNA. No translation available.
CH471053 Genomic DNA. Translation: EAW99490.1.
CH471053 Genomic DNA. Translation: EAW99492.1.
CH471053 Genomic DNA. Translation: EAW99493.1.
CH471053 Genomic DNA. Translation: EAW99494.1.
BC001384 mRNA. Translation: AAH01384.2.
BC067273 mRNA. Translation: AAH67273.1.
AF130096 mRNA. Translation: AAG35521.1. Different initiation.
AF161450 mRNA. Translation: AAF29010.1.
RefSeqNP_001243654.1. NM_001256725.1.
NP_001243655.1. NM_001256726.1.
NP_001243656.1. NM_001256727.1.
NP_001243657.1. NM_001256728.1.
NP_006581.2. NM_006590.3.
UniGeneHs.654745.

3D structure databases

ProteinModelPortalQ53GS9.
SMRQ53GS9. Positions 129-556.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115939. 73 interactions.
IntActQ53GS9. 38 interactions.
MINTMINT-4655337.
STRING9606.ENSP00000312981.

Protein family/group databases

MEROPSC19.972.

PTM databases

PhosphoSiteQ53GS9.

Polymorphism databases

DMDM88909655.

Proteomic databases

PaxDbQ53GS9.
PeptideAtlasQ53GS9.
PRIDEQ53GS9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000323701; ENSP00000312981; ENSG00000168883. [Q53GS9-1]
ENST00000409470; ENSP00000386864; ENSG00000168883. [Q53GS9-1]
ENST00000409766; ENSP00000386803; ENSG00000168883. [Q53GS9-3]
ENST00000450066; ENSP00000396133; ENSG00000168883. [Q53GS9-2]
GeneID10713.
KEGGhsa:10713.
UCSCuc002sqb.4. human. [Q53GS9-1]
uc010ysv.3. human.

Organism-specific databases

CTD10713.
GeneCardsGC02P085829.
HGNCHGNC:20071. USP39.
HPAHPA034823.
MIM611594. gene.
neXtProtNX_Q53GS9.
PharmGKBPA134905136.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG259163.
HOVERGENHBG079718.
InParanoidQ53GS9.
KOK12847.
OMASHINVYA.
OrthoDBEOG7KH9JG.
PhylomeDBQ53GS9.
TreeFamTF300610.

Gene expression databases

ArrayExpressQ53GS9.
BgeeQ53GS9.
CleanExHS_USP39.
GenevestigatorQ53GS9.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR015880. Znf_C2H2-like.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamPF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
SMARTSM00355. ZnF_C2H2. 1 hit.
[Graphical view]
PROSITEPS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiUSP39.
GenomeRNAi10713.
NextBio40671.
PROQ53GS9.
SOURCESearch...

Entry information

Entry nameSNUT2_HUMAN
AccessionPrimary (citable) accession number: Q53GS9
Secondary accession number(s): A8K086 expand/collapse secondary AC list , B3KM40, B4DHT4, D6W5L4, G5E9H0, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310
Entry history
Integrated into UniProtKB/Swiss-Prot: February 21, 2006
Last sequence update: February 21, 2006
Last modified: April 16, 2014
This is version 92 of the entry and version 2 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

Peptidase families

Classification of peptidase families and list of entries

MIM cross-references

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

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM