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Protein

U4/U6.U5 tri-snRNP-associated protein 2

Gene

USP39

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

Functioni

Plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the precatalytic spliceosome (PubMed:11350945, PubMed:26912367). Regulates AURKB mRNA levels, and thereby plays a role in cytokinesis and in the spindle checkpoint. Does not have ubiquitin-specific peptidase activity (PubMed:18728397).3 Publications

Caution

Lacks the conserved His and Cys residues that are essential for the activity of de-ubiquitinating enzymes. Lacks ubiquitin C-terminal hydrolase activity (PubMed:18728397).1 Publication1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri122 – 183UBP-typePROSITE-ProRule annotationAdd BLAST62

GO - Molecular functioni

GO - Biological processi

Keywordsi

Biological processCell cycle, Cell division, mRNA processing, mRNA splicing
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway

Protein family/group databases

MEROPSiC19.972

Names & Taxonomyi

Protein namesi
Recommended name:
U4/U6.U5 tri-snRNP-associated protein 2
Alternative name(s):
Inactive ubiquitin-specific peptidase 391 Publication
SAD1 homolog1 Publication
U4/U6.U5 tri-snRNP-associated 65 kDa protein1 Publication
Short name:
65K1 Publication
Gene namesi
Name:USP39
ORF Names:CGI-21, HSPC332, PRO2855
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000168883.19
HGNCiHGNC:20071 USP39
MIMi611594 gene
neXtProtiNX_Q53GS9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi10713
OpenTargetsiENSG00000168883
PharmGKBiPA134905136

Polymorphism and mutation databases

BioMutaiUSP39
DMDMi88909655

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002239621 – 565U4/U6.U5 tri-snRNP-associated protein 2Add BLAST565

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei46PhosphoserineCombined sources1
Cross-linki51Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei82PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ53GS9
MaxQBiQ53GS9
PaxDbiQ53GS9
PeptideAtlasiQ53GS9
PRIDEiQ53GS9
ProteomicsDBi62489

PTM databases

iPTMnetiQ53GS9
PhosphoSitePlusiQ53GS9
SwissPalmiQ53GS9

Expressioni

Gene expression databases

BgeeiENSG00000168883 Expressed in 212 organ(s), highest expression level in gastrocnemius
CleanExiHS_USP39
ExpressionAtlasiQ53GS9 baseline and differential
GenevisibleiQ53GS9 HS

Organism-specific databases

HPAiHPA034823

Interactioni

Subunit structurei

The U4/U6-U5 tri-snRNP complex is a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:11350945, PubMed:26912367). 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, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:16723661, PubMed:26912367).3 Publications

Protein-protein interaction databases

BioGridi115939, 97 interactors
CORUMiQ53GS9
IntActiQ53GS9, 45 interactors
MINTiQ53GS9
STRINGi9606.ENSP00000312981

Structurei

3D structure databases

ProteinModelPortaliQ53GS9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini225 – 555USPAdd BLAST331

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 103Arg-richAdd BLAST100

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri122 – 183UBP-typePROSITE-ProRule annotationAdd BLAST62

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG2026 Eukaryota
ENOG410XS41 LUCA
GeneTreeiENSGT00390000007992
HOGENOMiHOG000188754
HOVERGENiHBG079718
InParanoidiQ53GS9
KOiK12847
OMAiCNVVLHA
OrthoDBiEOG091G06U0
PhylomeDBiQ53GS9
TreeFamiTF300610

Family and domain databases

CDDicd02669 Peptidase_C19M, 1 hit
Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR038765 Papain_like_cys_pep_sf
IPR001394 Peptidase_C19_UCH
IPR033809 USP39
IPR028889 USP_dom
IPR013083 Znf_RING/FYVE/PHD
IPR001607 Znf_UBP
PANTHERiPTHR43985 PTHR43985, 1 hit
PfamiView protein in Pfam
PF00443 UCH, 1 hit
PF02148 zf-UBP, 1 hit
SMARTiView protein in SMART
SM00290 ZnF_UBP, 1 hit
SUPFAMiSSF54001 SSF54001, 1 hit
PROSITEiView protein in PROSITE
PS50235 USP_3, 1 hit
PS50271 ZF_UBP, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q53GS9-1) [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
MSGRSKRESR GSTRGKRESE SRGSSGRVKR ERDREREPEA ASSRGSPVRV
60 70 80 90 100
KREFEPASAR EAPASVVPFV RVKREREVDE DSEPEREVRA KNGRVDSEDR
110 120 130 140 150
RSRHCPYLDT INRSVLDFDF EKLCSISLSH INAYACLVCG KYFQGRGLKS
160 170 180 190 200
HAYIHSVQFS HHVFLNLHTL KFYCLPDNYE IIDSSLEDIT YVLKPTFTKQ
210 220 230 240 250
QIANLDKQAK LSRAYDGTTY LPGIVGLNNI KANDYANAVL QALSNVPPLR
260 270 280 290 300
NYFLEEDNYK NIKRPPGDIM FLLVQRFGEL MRKLWNPRNF KAHVSPHEML
310 320 330 340 350
QAVVLCSKKT FQITKQGDGV DFLSWFLNAL HSALGGTKKK KKTIVTDVFQ
360 370 380 390 400
GSMRIFTKKL PHPDLPAEEK EQLLHNDEYQ ETMVESTFMY LTLDLPTAPL
410 420 430 440 450
YKDEKEQLII PQVPLFNILA KFNGITEKEY KTYKENFLKR FQLTKLPPYL
460 470 480 490 500
IFCIKRFTKN NFFVEKNPTI VNFPITNVDL REYLSEEVQA VHKNTTYDLI
510 520 530 540 550
ANIVHDGKPS EGSYRIHVLH HGTGKWYELQ DLQVTDILPQ MITLSEAYIQ
560
IWKRRDNDET NQQGA
Length:565
Mass (Da):65,381
Last modified:February 21, 2006 - v2
Checksum:i8946FD5DCDEFD0B0
GO
Isoform 2 (identifier: Q53GS9-2) [UniParc]FASTAAdd to basket

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

Show »
Length:462
Mass (Da):53,510
Checksum:iC57BF48DC1B0F9D5
GO
Isoform 3 (identifier: Q53GS9-3) [UniParc]FASTAAdd to basket

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

Show »
Length:488
Mass (Da):56,359
Checksum:i757387284D021074
GO

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A087X1B2A0A087X1B2_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
487Annotation score:
B9A018B9A018_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
536Annotation score:
C9JIU2C9JIU2_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
129Annotation score:
C9J0X5C9J0X5_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
113Annotation score:
F8WC91F8WC91_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
154Annotation score:
A0A087WW31A0A087WW31_HUMAN
U4/U6.U5 tri-snRNP-associated prote...
USP39
61Annotation score:

Sequence cautioni

The sequence AAD27730 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence AAG35521 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti13T → I in BAD96572 (Ref. 4) Curated1
Sequence conflicti135A → V in BAD96572 (Ref. 4) Curated1
Sequence conflicti277F → S in BAG50852 (PubMed:14702039).Curated1
Sequence conflicti280L → P in BAG50852 (PubMed:14702039).Curated1
Sequence conflicti294V → A in BAG50852 (PubMed:14702039).Curated1
Sequence conflicti400L → F in AAK49524 (PubMed:11350945).Curated1
Sequence conflicti456R → I in AAD27730 (PubMed:10810093).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0451671 – 89MSGRS…EREVR → MLTAVPSHLFS in isoform 2. 1 PublicationAdd BLAST89
Alternative sequenceiVSP_045168113 – 144RSVLD…GKYFQ → SFSPFPT in isoform 2. 1 PublicationAdd BLAST32
Alternative sequenceiVSP_046822477 – 565NVDLR…NQQGA → GQANGMNYKTSR in isoform 3. 1 PublicationAdd BLAST89

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS33234.1 [Q53GS9-1]
CCDS58716.1 [Q53GS9-2]
CCDS58717.1 [Q53GS9-3]
RefSeqiNP_001243654.1, NM_001256725.1 [Q53GS9-1]
NP_001243655.1, NM_001256726.1 [Q53GS9-3]
NP_001243656.1, NM_001256727.1
NP_001243657.1, NM_001256728.1 [Q53GS9-2]
NP_006581.2, NM_006590.3 [Q53GS9-1]
XP_006711985.1, XM_006711922.1
XP_006711986.1, XM_006711923.2
XP_011530789.1, XM_011532487.1
XP_011530790.1, XM_011532488.1
XP_016858671.1, XM_017003182.1
UniGeneiHs.654745

Genome annotation databases

EnsembliENST00000323701; ENSP00000312981; ENSG00000168883 [Q53GS9-1]
ENST00000409470; ENSP00000386864; ENSG00000168883 [Q53GS9-1]
ENST00000409766; ENSP00000386803; ENSG00000168883 [Q53GS9-3]
ENST00000450066; ENSP00000396133; ENSG00000168883 [Q53GS9-2]
GeneIDi10713
KEGGihsa:10713
UCSCiuc002sqe.5 human [Q53GS9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS33234.1 [Q53GS9-1]
CCDS58716.1 [Q53GS9-2]
CCDS58717.1 [Q53GS9-3]
RefSeqiNP_001243654.1, NM_001256725.1 [Q53GS9-1]
NP_001243655.1, NM_001256726.1 [Q53GS9-3]
NP_001243656.1, NM_001256727.1
NP_001243657.1, NM_001256728.1 [Q53GS9-2]
NP_006581.2, NM_006590.3 [Q53GS9-1]
XP_006711985.1, XM_006711922.1
XP_006711986.1, XM_006711923.2
XP_011530789.1, XM_011532487.1
XP_011530790.1, XM_011532488.1
XP_016858671.1, XM_017003182.1
UniGeneiHs.654745

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00V1-565[»]
ProteinModelPortaliQ53GS9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115939, 97 interactors
CORUMiQ53GS9
IntActiQ53GS9, 45 interactors
MINTiQ53GS9
STRINGi9606.ENSP00000312981

Protein family/group databases

MEROPSiC19.972

PTM databases

iPTMnetiQ53GS9
PhosphoSitePlusiQ53GS9
SwissPalmiQ53GS9

Polymorphism and mutation databases

BioMutaiUSP39
DMDMi88909655

Proteomic databases

EPDiQ53GS9
MaxQBiQ53GS9
PaxDbiQ53GS9
PeptideAtlasiQ53GS9
PRIDEiQ53GS9
ProteomicsDBi62489

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000323701; ENSP00000312981; ENSG00000168883 [Q53GS9-1]
ENST00000409470; ENSP00000386864; ENSG00000168883 [Q53GS9-1]
ENST00000409766; ENSP00000386803; ENSG00000168883 [Q53GS9-3]
ENST00000450066; ENSP00000396133; ENSG00000168883 [Q53GS9-2]
GeneIDi10713
KEGGihsa:10713
UCSCiuc002sqe.5 human [Q53GS9-1]

Organism-specific databases

CTDi10713
DisGeNETi10713
EuPathDBiHostDB:ENSG00000168883.19
GeneCardsiUSP39
HGNCiHGNC:20071 USP39
HPAiHPA034823
MIMi611594 gene
neXtProtiNX_Q53GS9
OpenTargetsiENSG00000168883
PharmGKBiPA134905136
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2026 Eukaryota
ENOG410XS41 LUCA
GeneTreeiENSGT00390000007992
HOGENOMiHOG000188754
HOVERGENiHBG079718
InParanoidiQ53GS9
KOiK12847
OMAiCNVVLHA
OrthoDBiEOG091G06U0
PhylomeDBiQ53GS9
TreeFamiTF300610

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

ChiTaRSiUSP39 human
GeneWikiiUSP39
GenomeRNAii10713
PROiPR:Q53GS9
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168883 Expressed in 212 organ(s), highest expression level in gastrocnemius
CleanExiHS_USP39
ExpressionAtlasiQ53GS9 baseline and differential
GenevisibleiQ53GS9 HS

Family and domain databases

CDDicd02669 Peptidase_C19M, 1 hit
Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR038765 Papain_like_cys_pep_sf
IPR001394 Peptidase_C19_UCH
IPR033809 USP39
IPR028889 USP_dom
IPR013083 Znf_RING/FYVE/PHD
IPR001607 Znf_UBP
PANTHERiPTHR43985 PTHR43985, 1 hit
PfamiView protein in Pfam
PF00443 UCH, 1 hit
PF02148 zf-UBP, 1 hit
SMARTiView protein in SMART
SM00290 ZnF_UBP, 1 hit
SUPFAMiSSF54001 SSF54001, 1 hit
PROSITEiView protein in PROSITE
PS50235 USP_3, 1 hit
PS50271 ZF_UBP, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSNUT2_HUMAN
AccessioniPrimary (citable) accession number: Q53GS9
Secondary accession number(s): A8K086
, B3KM40, B4DHT4, D6W5L4, G5E9H0, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 21, 2006
Last sequence update: February 21, 2006
Last modified: October 10, 2018
This is version 135 of the entry and version 2 of the sequence. See 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 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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