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Protein

Regulator of nonsense transcripts 2

Gene

UPF2

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

Functioni

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA.3 Publications

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • telomeric DNA binding Source: BHF-UCL

GO - Biological processi

  • animal organ regeneration Source: Ensembl
  • liver development Source: Ensembl
  • mRNA export from nucleus Source: HGNC
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB

Keywordsi

Molecular functionRNA-binding
Biological processNonsense-mediated mRNA decay

Enzyme and pathway databases

ReactomeiR-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Protein family/group databases

MoonDBiQ9HAU5 Predicted

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 2
Alternative name(s):
Nonsense mRNA reducing factor 2
Up-frameshift suppressor 2 homolog
Short name:
hUpf2
Gene namesi
Name:UPF2
Synonyms:KIAA1408, RENT2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

EuPathDBiHostDB:ENSG00000151461.19
HGNCiHGNC:17854 UPF2
MIMi605529 gene
neXtProtiNX_Q9HAU5

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

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi796 – 797RK → EE: Strongly impairs RNA-binding. 1 Publication2
Mutagenesisi847D → K: Does not abolish interaction with UPF3B. 1 Publication1
Mutagenesisi851 – 852ED → KR: Does not abolish interaction with UPF3B. Does not abolish interaction with UPF3B; when associated with D-854. 1 Publication2
Mutagenesisi854R → D: Does not abolish interaction with UPF3B; when associated with K-851 and R-852. 1 Publication1
Mutagenesisi858E → R: Abolishes interaction with UPF3B and association with SMG1 and RBM8A; reduces phosphorylation of UPF1. 2 Publications1
Mutagenesisi894Y → A: Does not impair RNA-binding; when associated with A-932. 1 Publication1
Mutagenesisi932Y → A: Does not impair RNA-binding; when associated with A-894. 1 Publication1
Mutagenesisi1113F → E: Abolishes interaction with UPF1. 1
Mutagenesisi1120M → E: Decreases interaction with UPF1; does not reduce NMD efficiency. 1 Publication1
Mutagenesisi1121M → E: Decreases interaction with UPF1; does not reduce NMD efficiency. 1 Publication1
Mutagenesisi1123E → R: Decreases interaction with UPF1. 1 Publication1
Mutagenesisi1169M → E: Decreases interaction with UPF1. 1 Publication1
Mutagenesisi1171F → E: Abolishes interaction with UPF1; reduces NMD efficiency. 1 Publication1
Mutagenesisi1171F → E: Greatly reduces NMD efficiency; when associated with E-1173 and E-1174. 1 Publication1
Mutagenesisi1173M → E: Abolishes interaction with UPF1. 1 Publication1
Mutagenesisi1173M → E: Greatly reduces NMD efficiency; when associated with E-1171 and E-1174. 1 Publication1
Mutagenesisi1174L → E: Abolishes interaction with UPF1; reduces NMD efficiency. 1 Publication1
Mutagenesisi1174L → E: Greatly reduces NMD efficiency; when associated with E-1171 and E-1173. 1 Publication1
Mutagenesisi1176R → E: Decreases interaction with UPF1. 1 Publication1

Organism-specific databases

DisGeNETi26019
OpenTargetsiENSG00000151461
PharmGKBiPA134945630

Polymorphism and mutation databases

BioMutaiUPF2
DMDMi60390647

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000972481 – 1272Regulator of nonsense transcripts 2Add BLAST1272

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1088PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9HAU5
MaxQBiQ9HAU5
PaxDbiQ9HAU5
PeptideAtlasiQ9HAU5
PRIDEiQ9HAU5
ProteomicsDBi81440
81441 [Q9HAU5-2]

PTM databases

CarbonylDBiQ9HAU5
iPTMnetiQ9HAU5
PhosphoSitePlusiQ9HAU5

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

BgeeiENSG00000151461 Expressed in 231 organ(s), highest expression level in testis
GenevisibleiQ9HAU5 HS

Organism-specific databases

HPAiHPA067008

Interactioni

Subunit structurei

Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with SMG1, EST1A, UPF1, UPF3A, UPF3B, EIF4A1 and EIF1.10 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi117490, 94 interactors
CORUMiQ9HAU5
DIPiDIP-31148N
IntActiQ9HAU5, 41 interactors
MINTiQ9HAU5
STRINGi9606.ENSP00000348708

Structurei

Secondary structure

11272
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

DisProtiDP00949
ProteinModelPortaliQ9HAU5
SMRiQ9HAU5
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9HAU5

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini168 – 431MIF4G 1Add BLAST264
Domaini569 – 758MIF4G 2Add BLAST190
Domaini773 – 986MIF4G 3Add BLAST214

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni94 – 133Sufficient for interaction with UPF1Add BLAST40
Regioni711 – 928Sufficient for interaction with UPF3A and UPF3BAdd BLAST218
Regioni757 – 1272Sufficient for interaction with EIF4A1 and EIF11 PublicationAdd BLAST516
Regioni839 – 859Binds to UPF3BAdd BLAST21
Regioni1084 – 1272Sufficient for interaction with UPF1 C-terminusAdd BLAST189
Regioni1105 – 1198Necessary for interaction with UPF1Add BLAST94
Regioni1105 – 1129Interaction with UPF1Add BLAST25
Regioni1167 – 1207Interaction with UPF1Add BLAST41

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili54 – 134Sequence analysisAdd BLAST81
Coiled coili487 – 559Sequence analysisAdd BLAST73

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi6 – 136Glu/Lys-richAdd BLAST131
Compositional biasi1025 – 1094Glu-richAdd BLAST70

Keywords - Domaini

Coiled coil, Repeat

Phylogenomic databases

eggNOGiKOG2051 Eukaryota
ENOG410XQ1E LUCA
GeneTreeiENSGT00530000064318
HOVERGENiHBG079124
InParanoidiQ9HAU5
KOiK14327
OMAiLVFFQHY
OrthoDBiEOG091G01PX
PhylomeDBiQ9HAU5
TreeFamiTF300543

Family and domain databases

Gene3Di1.25.40.180, 3 hits
InterProiView protein in InterPro
IPR016024 ARM-type_fold
IPR016021 MIF4-like_sf
IPR003890 MIF4G-like_typ-3
IPR039762 Nmd2/UPF2
IPR007193 Upf2/Nmd2_C
PANTHERiPTHR12839 PTHR12839, 1 hit
PfamiView protein in Pfam
PF02854 MIF4G, 3 hits
PF04050 Upf2, 1 hit
SMARTiView protein in SMART
SM00543 MIF4G, 3 hits
SUPFAMiSSF48371 SSF48371, 3 hits

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q9HAU5-1) [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
MPAERKKPAS MEEKDSLPNN KEKDCSERRT VSSKERPKDD IKLTAKKEVS
60 70 80 90 100
KAPEDKKKRL EDDKRKKEDK ERKKKDEEKV KAEEESKKKE EEEKKKHQEE
110 120 130 140 150
ERKKQEEQAK RQQEEEAAAQ MKEKEESIQL HQEAWERHHL RKELRSKNQN
160 170 180 190 200
APDSRPEENF FSRLDSSLKK NTAFVKKLKT ITEQQRDSLS HDFNGLNLSK
210 220 230 240 250
YIAEAVASIV EAKLKISDVN CAVHLCSLFH QRYADFAPSL LQVWKKHFEA
260 270 280 290 300
RKEEKTPNIT KLRTDLRFIA ELTIVGIFTD KEGLSLIYEQ LKNIINADRE
310 320 330 340 350
SHTHVSVVIS FCRHCGDDIA GLVPRKVKSA AEKFNLSFPP SEIISPEKQQ
360 370 380 390 400
PFQNLLKEYF TSLTKHLKRD HRELQNTERQ NRRILHSKGE LSEDRHKQYE
410 420 430 440 450
EFAMSYQKLL ANSQSLADLL DENMPDLPQD KPTPEEHGPG IDIFTPGKPG
460 470 480 490 500
EYDLEGGIWE DEDARNFYEN LIDLKAFVPA ILFKDNEKSC QNKESNKDDT
510 520 530 540 550
KEAKESKENK EVSSPDDLEL ELENLEINDD TLELEGGDEA EDLTKKLLDE
560 570 580 590 600
QEQEDEEAST GSHLKLIVDA FLQQLPNCVN RDLIDKAAMD FCMNMNTKAN
610 620 630 640 650
RKKLVRALFI VPRQRLDLLP FYARLVATLH PCMSDVAEDL CSMLRGDFRF
660 670 680 690 700
HVRKKDQINI ETKNKTVRFI GELTKFKMFT KNDTLHCLKM LLSDFSHHHI
710 720 730 740 750
EMACTLLETC GRFLFRSPES HLRTSVLLEQ MMRKKQAMHL DARYVTMVEN
760 770 780 790 800
AYYYCNPPPA EKTVKKKRPP LQEYVRKLLY KDLSKVTTEK VLRQMRKLPW
810 820 830 840 850
QDQEVKDYVI CCMINIWNVK YNSIHCVANL LAGLVLYQED VGIHVVDGVL
860 870 880 890 900
EDIRLGMEVN QPKFNQRRIS SAKFLGELYN YRMVESAVIF RTLYSFTSFG
910 920 930 940 950
VNPDGSPSSL DPPEHLFRIR LVCTILDTCG QYFDRGSSKR KLDCFLVYFQ
960 970 980 990 1000
RYVWWKKSLE VWTKDHPFPI DIDYMISDTL ELLRPKIKLC NSLEESIRQV
1010 1020 1030 1040 1050
QDLEREFLIK LGLVNDKDSK DSMTEGENLE EDEEEEEGGA ETEEQSGNES
1060 1070 1080 1090 1100
EVNEPEEEEG SDNDDDEGEE EEEENTDYLT DSNKENETDE ENTEVMIKGG
1110 1120 1130 1140 1150
GLKHVPCVED EDFIQALDKM MLENLQQRSG ESVKVHQLDV AIPLHLKSQL
1160 1170 1180 1190 1200
RKGPPLGGGE GEAESADTMP FVMLTRKGNK QQFKILNVPM SSQLAANHWN
1210 1220 1230 1240 1250
QQQAEQEERM RMKKLTLDIN ERQEQEDYQE MLQSLAQRPA PANTNRERRP
1260 1270
RYQHPKGAPN ADLIFKTGGR RR
Length:1,272
Mass (Da):147,810
Last modified:March 1, 2001 - v1
Checksum:i95F3C57D2854BB44
GO
Isoform 2 (identifier: Q9HAU5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     54-83: Missing.
     588-609: AMDFCMNMNTKANRKKLVRALF → EKAFCNGNLARVNLLLRMAVKK
     610-1272: Missing.

Note: No experimental confirmation available.
Show »
Length:579
Mass (Da):66,842
Checksum:iFA8367F0C864C24E
GO

Sequence cautioni

The sequence BAA92646 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti119A → T in BAC04721 (PubMed:14702039).Curated1
Sequence conflicti338F → L in BAC04721 (PubMed:14702039).Curated1
Sequence conflicti844H → Q in AAG48509 (PubMed:11163187).Curated1
Sequence conflicti844H → Q in BAA92646 (PubMed:10718198).Curated1
Sequence conflicti969P → S in BAA92646 (PubMed:10718198).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_024345496N → S. Corresponds to variant dbSNP:rs7079388Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01295854 – 83Missing in isoform 2. 1 PublicationAdd BLAST30
Alternative sequenceiVSP_012959588 – 609AMDFC…VRALF → EKAFCNGNLARVNLLLRMAV KK in isoform 2. 1 PublicationAdd BLAST22
Alternative sequenceiVSP_012960610 – 1272Missing in isoform 2. 1 PublicationAdd BLAST663

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF301013 mRNA Translation: AAG33225.1
AY013249 mRNA Translation: AAG48509.1
AF318574 mRNA Translation: AAG60689.1
AB037829 mRNA Translation: BAA92646.1 Different initiation.
AK000764 mRNA Translation: BAA91369.1
AK096191 mRNA Translation: BAC04721.1
AC073160 Genomic DNA No translation available.
AL138898 Genomic DNA No translation available.
AL645617 Genomic DNA No translation available.
CH471072 Genomic DNA Translation: EAW86329.1
CH471072 Genomic DNA Translation: EAW86330.1
CH471072 Genomic DNA Translation: EAW86332.1
CH471072 Genomic DNA Translation: EAW86333.1
BC114964 mRNA Translation: AAI14965.1
BC115737 mRNA Translation: AAI15738.1
AL080198 mRNA Translation: CAB45771.1
CCDSiCCDS7086.1 [Q9HAU5-1]
PIRiT12507
RefSeqiNP_056357.1, NM_015542.3 [Q9HAU5-1]
NP_542166.1, NM_080599.2 [Q9HAU5-1]
UniGeneiHs.370689
Hs.610110
Hs.732383

Genome annotation databases

EnsembliENST00000356352; ENSP00000348708; ENSG00000151461 [Q9HAU5-1]
ENST00000357604; ENSP00000350221; ENSG00000151461 [Q9HAU5-1]
ENST00000397053; ENSP00000380244; ENSG00000151461 [Q9HAU5-1]
GeneIDi26019
KEGGihsa:26019
UCSCiuc001ila.3 human [Q9HAU5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF301013 mRNA Translation: AAG33225.1
AY013249 mRNA Translation: AAG48509.1
AF318574 mRNA Translation: AAG60689.1
AB037829 mRNA Translation: BAA92646.1 Different initiation.
AK000764 mRNA Translation: BAA91369.1
AK096191 mRNA Translation: BAC04721.1
AC073160 Genomic DNA No translation available.
AL138898 Genomic DNA No translation available.
AL645617 Genomic DNA No translation available.
CH471072 Genomic DNA Translation: EAW86329.1
CH471072 Genomic DNA Translation: EAW86330.1
CH471072 Genomic DNA Translation: EAW86332.1
CH471072 Genomic DNA Translation: EAW86333.1
BC114964 mRNA Translation: AAI14965.1
BC115737 mRNA Translation: AAI15738.1
AL080198 mRNA Translation: CAB45771.1
CCDSiCCDS7086.1 [Q9HAU5-1]
PIRiT12507
RefSeqiNP_056357.1, NM_015542.3 [Q9HAU5-1]
NP_542166.1, NM_080599.2 [Q9HAU5-1]
UniGeneiHs.370689
Hs.610110
Hs.732383

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UW4X-ray1.95B/D768-1015[»]
2WJVX-ray2.85D/E1105-1198[»]
4CEKX-ray2.35A455-757[»]
4CEMX-ray2.60A/B121-486[»]
DisProtiDP00949
ProteinModelPortaliQ9HAU5
SMRiQ9HAU5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117490, 94 interactors
CORUMiQ9HAU5
DIPiDIP-31148N
IntActiQ9HAU5, 41 interactors
MINTiQ9HAU5
STRINGi9606.ENSP00000348708

Protein family/group databases

MoonDBiQ9HAU5 Predicted

PTM databases

CarbonylDBiQ9HAU5
iPTMnetiQ9HAU5
PhosphoSitePlusiQ9HAU5

Polymorphism and mutation databases

BioMutaiUPF2
DMDMi60390647

Proteomic databases

EPDiQ9HAU5
MaxQBiQ9HAU5
PaxDbiQ9HAU5
PeptideAtlasiQ9HAU5
PRIDEiQ9HAU5
ProteomicsDBi81440
81441 [Q9HAU5-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000356352; ENSP00000348708; ENSG00000151461 [Q9HAU5-1]
ENST00000357604; ENSP00000350221; ENSG00000151461 [Q9HAU5-1]
ENST00000397053; ENSP00000380244; ENSG00000151461 [Q9HAU5-1]
GeneIDi26019
KEGGihsa:26019
UCSCiuc001ila.3 human [Q9HAU5-1]

Organism-specific databases

CTDi26019
DisGeNETi26019
EuPathDBiHostDB:ENSG00000151461.19
GeneCardsiUPF2
HGNCiHGNC:17854 UPF2
HPAiHPA067008
MIMi605529 gene
neXtProtiNX_Q9HAU5
OpenTargetsiENSG00000151461
PharmGKBiPA134945630
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2051 Eukaryota
ENOG410XQ1E LUCA
GeneTreeiENSGT00530000064318
HOVERGENiHBG079124
InParanoidiQ9HAU5
KOiK14327
OMAiLVFFQHY
OrthoDBiEOG091G01PX
PhylomeDBiQ9HAU5
TreeFamiTF300543

Enzyme and pathway databases

ReactomeiR-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Miscellaneous databases

ChiTaRSiUPF2 human
EvolutionaryTraceiQ9HAU5
GeneWikiiUPF2
GenomeRNAii26019
PROiPR:Q9HAU5
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000151461 Expressed in 231 organ(s), highest expression level in testis
GenevisibleiQ9HAU5 HS

Family and domain databases

Gene3Di1.25.40.180, 3 hits
InterProiView protein in InterPro
IPR016024 ARM-type_fold
IPR016021 MIF4-like_sf
IPR003890 MIF4G-like_typ-3
IPR039762 Nmd2/UPF2
IPR007193 Upf2/Nmd2_C
PANTHERiPTHR12839 PTHR12839, 1 hit
PfamiView protein in Pfam
PF02854 MIF4G, 3 hits
PF04050 Upf2, 1 hit
SMARTiView protein in SMART
SM00543 MIF4G, 3 hits
SUPFAMiSSF48371 SSF48371, 3 hits
ProtoNetiSearch...

Entry informationi

Entry nameiRENT2_HUMAN
AccessioniPrimary (citable) accession number: Q9HAU5
Secondary accession number(s): A6NLJ5
, D3DRS0, Q14BM1, Q5W0J4, Q8N8U1, Q9H1J2, Q9NWL1, Q9P2D9, Q9Y4M9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2001
Last modified: November 7, 2018
This is version 163 of the entry and version 1 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
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