Q9VM71 (XRN2_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
5'-3' exoribonuclease 2 homolog
EC=3.1.13.-

Alternative name(s):
Ribonucleic acid-trafficking protein 1
Short name=dRAT1

Gene names

Name:	Rat1
ORF Names:	CG10354

Organism

Drosophila melanogaster (Fruit fly) [Reference proteome]

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Panarthropoda › Arthropoda › Mandibulata › Pancrustacea › Hexapoda › Insecta › Dicondylia › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Eremoneura › Cyclorrhapha › Schizophora › Acalyptratae › Ephydroidea › Drosophilidae › Drosophilinae › Drosophilini › Drosophilina › Drosophiliti › Drosophila › Sophophora › melanogaster group › melanogaster subgroup

Protein attributes

Sequence length	908 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Possesses 5'->3' exoribonuclease activity. May promote the termination of transcription by RNA polymerase II By similarity.
Catalytic activity	Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.
Subunit structure	Does not interact with cuff.
Subcellular location	Nucleus Ref.4.
Sequence similarities	Belongs to the 5'-3' exonuclease family. XRN2/RAT1 subfamily. Contains 1 CCHC-type zinc finger.
Sequence caution	The sequence AAX33482.1 differs from that shown. Reason: Erroneous termination at position 520. Translated as Gln.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Transcription termination mRNA processing
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Exonuclease Hydrolase Nuclease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA catabolic process, exonucleolytic Inferred from sequence or structural similarity. Source: UniProtKB DNA-dependent transcription, termination Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW neurogenesis Inferred from mutant phenotype PubMed 21549331. Source: FlyBase regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from direct assay Ref.4. Source: UniProtKB
Molecular_function	5'-3' exonuclease activity Inferred from sequence or structural similarity. Source: UniProtKB 5'-3' exoribonuclease activity Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 908	908	5'-3' exoribonuclease 2 homolog		PRO_0000249914
Regions
	Zinc finger	263 – 280	18	CCHC-type
	Compositional bias	799 – 825	27	Gly-rich
	Compositional bias	812 – 903	92	Gln-rich
Amino acid modifications
	Modified residue	438	1	Phosphoserine Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Q9VM71 [UniParc]. Last modified March 1, 2001. Version 2. Checksum: D9D113DB6630DD0F	FASTA	908	103,960
	10 20 30 40 50 60 MGVPAFFRWL SRKYPSVIIE CNENKQVDAD TGRNIYEDPT LPNPNGIEFD NLYLDMNGII 70 80 90 100 110 120 HPCTHPEDKP APKNEDEMMV AIFECIDRLF GIVRPRKLLY MAIDGVAPRA KMNQQRSRRF 130 140 150 160 170 180 RAAKETTEKR LEIARIREEL LSRGCKLPPE KEKGEHFDSN CITPGTPFMD RLSKCLHYFV 190 200 210 220 230 240 HDRQNNNPAW KGIKVILSDA NVPGEGEHKI MDYIRKQRAQ PDHDPNTQHV LCGADADLIM 250 260 270 280 290 300 LGLATHEPNF TIIREEFLPN KPRPCDICNG FGHEMDKCVG LGATAPTSAN FKPDVPIGAE 310 320 330 340 350 360 VKFIFVRLSV LREYLKQTLE MPNLPFEYSF ERALDDWVFM CFFVGNDFLP HLPSLEIREG 370 380 390 400 410 420 AVDRLVELYK KCVYKTRGYL TDSGDVNLDR VQLIMTDLGN AEDQIFKSRQ RREEQFKARD 430 440 450 460 470 480 KARKRQERNQ DHGSLNQSAF GASAVGPNSQ QRSVGNYKEE AAALRNRKRT SDMANLDDED 490 500 510 520 530 540 EEENNDEVRL WEDGFKDRYY ESKFDVAPGN QQFRYAVALQ YVRGLCWVLK YYYQGCASWN 550 560 570 580 590 600 WYFPYHYAPF ASDFVNIQGL STMFEKGTKP FNPLEQLMGV FPAASSSHVP EPWAKLMSDP 610 620 630 640 650 660 ESPIIDFYPE DFKIDLNGKK FAWQGVALLP FVDEKRLFKA LVPYYDQLTG EEVKRNKRGD 670 680 690 700 710 720 NYLYISNQSP HYKKVKKISE KDDESVCKAI SFDGMRGTLG KTELNTAISG VLKSPISGLS 730 740 750 760 770 780 DINDNITVTT TFRDPEYDED YIFEAKRLEN AVDPPQVLPN EQSGNKHRPV IGFNSHLTRA 790 800 810 820 830 840 YVPDSGHRML NAGIRNQQGG GGNGGGGGGY GQGGGYGQGI GGNQGQSYQN NSRNYNYNYN 850 860 870 880 890 900 NNYNQHQGGG YQNNYNNRQQ QQYGHNQRFN QDNSNQQQRN FNNYNGPRNN NYQQQGGSRQ QNQNYRRF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of Drosophila melanogaster." Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D. , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C. Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[2]	"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review." Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E. Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION. Strain: Berkeley.
[3]	Stapleton M., Carlson J.W., Booth B., Chavez C., Frise E., George R.A., Pacleb J.M., Park S., Wan K.H., Yu C., Rubin G.M., Celniker S.E. Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Berkeley. Tissue: Embryo.
[4]	"Cutoff and aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila." Chen Y., Pane A., Schuepbach T. Curr. Biol. 17:637-642(2007) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION, SUBCELLULAR LOCATION, NO INTERACTION WITH CUFF.
[5]	"Phosphoproteome analysis of Drosophila melanogaster embryos." Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P. J. Proteome Res. 7:1675-1682(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-438, MASS SPECTROMETRY. Tissue: Embryo.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE014134 Genomic DNA. Translation: AAF52452.2. BT021334 mRNA. Translation: AAX33482.1. Sequence problems. BT056259 mRNA. Translation: ACL68706.1.
RefSeq	NP_001260166.1. NM_001273237.1. NP_609082.1. NM_135238.3.
UniGene	Dm.8576.
3D structure databases
ProteinModelPortal	Q9VM71.
SMR	Q9VM71. Positions 1-415, 476-761.
ModBase	Search...
Protein-protein interaction databases
MINT	MINT-855535.
Proteomic databases
PaxDb	Q9VM71.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	FBtr0079345; FBpp0078973; FBgn0031868. FBtr0332324; FBpp0304602; FBgn0031868.
GeneID	33964.
KEGG	dme:Dmel_CG10354.
UCSC	CG10354-RA. d. melanogaster.
Organism-specific databases
CTD	33964.
FlyBase	FBgn0031868. Rat1.
Phylogenomic databases
eggNOG	COG5049.
GeneTree	ENSGT00670000098098.
InParanoid	Q9VM71.
KO	K12619.
OMA	RKRMKRD.
OrthoDB	EOG41VHHV.
PhylomeDB	Q9VM71.
Gene expression databases
Bgee	Q9VM71.
GermOnline	CG10354. Drosophila melanogaster.
Family and domain databases
InterPro	IPR027073. 5_3_exoribonuclease. IPR017151. 5_3_exoribonuclease_2. IPR004859. Put_53exo. [Graphical view]
PANTHER	PTHR12341. PTHR12341. 1 hit.
Pfam	PF03159. XRN_N. 1 hit. [Graphical view]
PIRSF	PIRSF037239. Exonuclease_Xrn2. 1 hit.
PROSITE	PS50158. ZF_CCHC. False negative. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	33964.
NextBio	786169.

Entry information

Entry name

XRN2_DROME

Accession

Primary (citable) accession number: Q9VM71
Secondary accession number(s): B8A3W7, Q5BI90

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2006
Last sequence update:	March 1, 2001
Last modified:	May 1, 2013
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project