Q53GS9 (SNUT2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	565 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
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.

Ontologies

Keywords
Biological process	Cell cycle Cell division mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Domain	Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW spliceosomal complex assembly Traceable author statement PubMed 10022888. Source: ProtInc ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	spliceosomal complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 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

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 565	565	U4/U6.U5 tri-snRNP-associated protein 2		PRO_0000223962
Regions
	Zinc finger	122 – 183	62	UBP-type
	Compositional bias	4 – 103	100	Arg-rich
Amino acid modifications
	Modified residue	82	1	Phosphoserine Ref.10 Ref.14 Ref.16
Natural variations
	Alternative sequence	1 – 89	89	MSGRS…EREVR → MLTAVPSHLFS in isoform 2.		VSP_045167
	Alternative sequence	113 – 144	32	RSVLD…GKYFQ → SFSPFPT in isoform 2.		VSP_045168
Experimental info
	Sequence conflict	13	1	T → I in BAD96572. Ref.4
	Sequence conflict	135	1	A → V in BAD96572. Ref.4
	Sequence conflict	400	1	L → F in AAK49524. Ref.1
	Sequence conflict	456	1	R → I in AAD27730. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 21, 2006. Version 2. Checksum: 8946FD5DCDEFD0B0	FASTA	565	65,381
	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
	Isoform 2 [UniParc]. Checksum: C57BF48DC1B0F9D5	FASTA	462	53,510
	10 20 30 40 50 60 MLTAVPSHLF SAKNGRVDSE DRRSRHCPYL DTINSFSPFP TGRGLKSHAY IHSVQFSHHV 70 80 90 100 110 120 FLNLHTLKFY CLPDNYEIID SSLEDITYVL KPTFTKQQIA NLDKQAKLSR AYDGTTYLPG 130 140 150 160 170 180 IVGLNNIKAN DYANAVLQAL SNVPPLRNYF LEEDNYKNIK RPPGDIMFLL VQRFGELMRK 190 200 210 220 230 240 LWNPRNFKAH VSPHEMLQAV VLCSKKTFQI TKQGDGVDFL SWFLNALHSA LGGTKKKKKT 250 260 270 280 290 300 IVTDVFQGSM RIFTKKLPHP DLPAEEKEQL LHNDEYQETM VESTFMYLTL DLPTAPLYKD 310 320 330 340 350 360 EKEQLIIPQV PLFNILAKFN GITEKEYKTY KENFLKRFQL TKLPPYLIFC IKRFTKNNFF 370 380 390 400 410 420 VEKNPTIVNF PITNVDLREY LSEEVQAVHK NTTYDLIANI VHDGKPSEGS YRIHVLHHGT 430 440 450 460 GKWYELQDLQ VTDILPQMIT LSEAYIQIWK RRDNDETNQQ GA

References

	« Hide 'large scale' referencesShow '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. , 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 AND 2). Tissue: Caudate nucleus.
[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. , 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. , 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, MASS SPECTROMETRY. 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, MASS SPECTROMETRY. 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, MASS SPECTROMETRY.
+	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. 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. BC001384 mRNA. Translation: AAH01384.2. BC067273 mRNA. Translation: AAH67273.1. AF130096 mRNA. Translation: AAG35521.1. Different initiation. AF161450 mRNA. Translation: AAF29010.1.
IPI	IPI00419844.
RefSeq	NP_001243654.1. NM_001256725.1. NP_001243656.1. NM_001256727.1. NP_001243657.1. NM_001256728.1. NP_006581.2. NM_006590.3.
UniGene	Hs.654745.
3D structure databases
ProteinModelPortal	Q53GS9.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q53GS9. 33 interactions.
STRING	9606.ENSP00000312981.
Protein family/group databases
MEROPS	C19.972.
PTM databases
PhosphoSite	Q53GS9.
Polymorphism databases
DMDM	88909655.
Proteomic databases
PaxDb	Q53GS9.
PeptideAtlas	Q53GS9.
PRIDE	Q53GS9.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000323701; ENSP00000312981; ENSG00000168883. ENST00000409470; ENSP00000386864; ENSG00000168883. ENST00000450066; ENSP00000396133; ENSG00000168883.
GeneID	10713.
KEGG	hsa:10713.
UCSC	uc002sqb.3. human.
Organism-specific databases
CTD	10713.
GeneCards	GC02P085829.
HGNC	HGNC:20071. USP39.
HPA	HPA034823.
MIM	611594. gene.
neXtProt	NX_Q53GS9.
PharmGKB	PA134905136.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG259163.
HOVERGEN	HBG079718.
InParanoid	Q53GS9.
KO	K12847.
OMA	SHINVYA.
OrthoDB	EOG4C5CJ7.
PhylomeDB	Q53GS9.
Gene expression databases
ArrayExpress	Q53GS9.
Bgee	Q53GS9.
CleanEx	HS_USP39.
Genevestigator	Q53GS9.
GermOnline	ENSG00000168883. Homo sapiens.
Family and domain databases
Gene3D	3.30.40.10. 1 hit.
InterPro	IPR001394. Peptidase_C19. IPR015880. Znf_C2H2-like. IPR013083. Znf_RING/FYVE/PHD. IPR001607. Znf_UBP. [Graphical view]
Pfam	PF00443. UCH. 1 hit. PF02148. zf-UBP. 1 hit. [Graphical view]
SMART	SM00355. ZnF_C2H2. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. False negative. PS00973. UCH_2_2. False negative. PS50235. UCH_2_3. 1 hit. PS50271. ZF_UBP. 1 hit. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	10713.
NextBio	40671.
SOURCE	Search...

Entry information

Entry name

SNUT2_HUMAN

Accession

Primary (citable) accession number: Q53GS9
Secondary accession number(s): A8K086 , B4DHT4, D6W5L4, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 21, 2006
Last sequence update:	February 21, 2006
Last modified:	May 1, 2013
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.