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Q9DBR1 (XRN2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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:
5'-3' exoribonuclease 2

EC=3.1.13.-
Alternative name(s):
Protein Dhm1
Gene names
Name:Xrn2
Synonyms:Dhm1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length951 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Possesses 5'->3' exoribonuclease activity. May promote the termination of transcription by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5' fragment which is subsequently processed to form the mature mRNA and a 3' fragment which remains attached to the elongating polymerase. The processive degradation of this 3' fragment by this protein may promote termination of transcription By similarity.

Catalytic activity

Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.

Subcellular location

Nucleusnucleolus By similarity.

Tissue specificity

Expressed in the spleen, testis, heart, brain, lung, liver, skeletal muscle, and kidney. Ref.1

Sequence similarities

Belongs to the 5'-3' exonuclease family. XRN2/RAT1 subfamily.

Contains 1 CCHC-type zinc finger.

Sequence caution

The sequence AAH04028.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processmRNA processing
Transcription
Transcription regulation
Transcription termination
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Molecular functionExonuclease
Hydrolase
Nuclease
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA catabolic process, exonucleolytic

Inferred from sequence or structural similarity. Source: UniProtKB

DNA recombination

Non-traceable author statement Ref.1. Source: UniProtKB

DNA repair

Non-traceable author statement Ref.1. Source: UniProtKB

DNA-templated transcription, termination

Inferred from electronic annotation. Source: UniProtKB-KW

RNA metabolic process

Inferred from genetic interaction Ref.1. Source: UniProtKB

RNA phosphodiester bond hydrolysis, exonucleolytic

Non-traceable author statement Ref.1. Source: GOC

cell growth

Inferred from genetic interaction Ref.1. Source: UniProtKB

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

microtubule-based process

Traceable author statement Ref.1. Source: UniProtKB

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

spermatogenesis

Inferred from expression pattern Ref.1. Source: UniProtKB

   Cellular_componentaggresome

Inferred from electronic annotation. Source: Ensembl

nucleolus

Inferred from sequence or structural similarity. Source: UniProtKB

nucleus

Inferred by curator Ref.1. Source: UniProtKB

   Molecular_function5'-3' exonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

5'-3' exoribonuclease activity

Non-traceable author statement Ref.1. Source: UniProtKB

nucleic acid binding

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: Q9DBR1-1)

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: Q9DBR1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     931-951: GYPREGRKYPLPPPSGRYSWN → VISTMWAVEGKQHTAHC
Note: No experimental confirmation available. May result from the retention of an intron in the cDNA.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 9519515'-3' exoribonuclease 2
PRO_0000071397

Regions

Zinc finger262 – 27817CCHC-type

Amino acid modifications

Modified residue2861N6-acetyllysine Ref.8
Modified residue4391Phosphothreonine By similarity
Modified residue4481Phosphoserine Ref.4 Ref.6
Modified residue4711Phosphoserine By similarity
Modified residue4731Phosphoserine By similarity
Modified residue4751Phosphoserine By similarity
Modified residue4991Phosphoserine Ref.4 Ref.6 Ref.7
Modified residue5011Phosphoserine Ref.4 Ref.6 Ref.7

Natural variations

Alternative sequence931 – 95121GYPRE…RYSWN → VISTMWAVEGKQHTAHC in isoform 2.
VSP_007235

Experimental info

Sequence conflict122 – 1243SKE → IKG in BAA07524. Ref.1
Sequence conflict2211H → Q in BAA07524. Ref.1
Sequence conflict3061L → P in BAE40020. Ref.2
Sequence conflict3321I → N in BAA07524. Ref.1
Sequence conflict3361V → E in BAA07524. Ref.1
Sequence conflict4401P → H in BAE40020. Ref.2
Sequence conflict4491P → Q in BAE40020. Ref.2
Sequence conflict4931K → R in BAA07524. Ref.1
Sequence conflict5631Y → L in BAA07524. Ref.1
Sequence conflict7121P → H in BAC27318. Ref.2
Sequence conflict7341T → K in BAC27318. Ref.2
Sequence conflict8371P → L in BAA07524. Ref.1
Sequence conflict8661Q → K in BAA07524. Ref.1
Sequence conflict8891P → H in BAC27318. Ref.2
Sequence conflict9231D → G in BAE40020. Ref.2
Sequence conflict9301Q → QV in BAC27318. Ref.2

Sequences

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

Last modified June 1, 2001. Version 1.
Checksum: CF57479291DD18B9

FASTA951108,687
        10         20         30         40         50         60 
MGVPAFFRWL SRKYPSIIVN CVEEKPKECN GVKIPVDASK PNPNDVEFDN LYLDMNGIIH 

        70         80         90        100        110        120 
PCTHPEDKPA PKNEDEMMVA IFEYIDRLFN IVRPRRLLYM AIDGVAPRAK MNQQRSRRFR 

       130        140        150        160        170        180 
ASKEGMEAAV EKQRVREEIL AKGGFLPPEE IKERFDSNCI TPGTEFMDNL AKCLRYYIAD 

       190        200        210        220        230        240 
RLNNDPGWKN LTVILSDASA PGEGEHKIMD YIRRQRAQPN HDPNTHHCLC GADADLIMLG 

       250        260        270        280        290        300 
LATHEPNFTI IREEFKPNKP KPCALCNQFG HEVKDCEGLP REKKGKHDEL ADSLPCAEGE 

       310        320        330        340        350        360 
FIFLRLNVLR EYLERELTMA SLPFPFDVER SIDDWVFMCF FVGNDFLPHL PSLEIREGAI 

       370        380        390        400        410        420 
DRLVNIYKNV VHKTGGYLTE SGYVNLQRVQ MIMLAVGEVE DSIFKKRKDD EDSFRRRQKE 

       430        440        450        460        470        480 
KRKRMKRDQP AFTPSGILTP HALGSRNSPG CQVASNPRQA AYEMRMQRNS SPSISPNTSF 

       490        500        510        520        530        540 
ASDGSPSPLG GIKRKAEDSD SEPEPEDNVR LWEAGWKQRY YKNKFDVDAA DEKFRRKVVQ 

       550        560        570        580        590        600 
SYVEGLCWVL RYYYQGCASW KWYYPFHYAP FASDFEGIAD MSSEFEKGTK PFKPLEQLMG 

       610        620        630        640        650        660 
VFPAASGNFL PPTWRKLMSD PDSSIIDFYP EDFAIDLNGK KYAWQGVALL PFVDERRLRA 

       670        680        690        700        710        720 
ALEEVYPDLT PEENRRNSLG GDVLFVGKLH PLRDFILELY QTGSTEPVDV PPELCHGIQG 

       730        740        750        760        770        780 
TFSLDEEAIL PDQTVCSPVP MLRDLTQNTA VSINFKDPQF AEDYVFKAAM LPGARKPATV 

       790        800        810        820        830        840 
LKPGDWEKSS NGRQWKPQLG FNRDRRPVHL DQAAFRTLGH VTPRGSGTSV YTNTALPPAN 

       850        860        870        880        890        900 
YQGNNYRPLL RGQAQIPKLM SNMRPQDSWR GPPPLFQQHR FERSVGAEPL LPWNRMIQNQ 

       910        920        930        940        950 
NAAFQPNQYQ MLGGPGGYPP RRDDHRGGRQ GYPREGRKYP LPPPSGRYSW N 

« Hide

Isoform 2 [UniParc].

Checksum: D07EDE545BB57F24
Show »

FASTA947108,108

References

« Hide 'large scale' references
[1]"Characterization of cDNA encoding mouse homolog of fission yeast dhp1+ gene: structural and functional conservation."
Shobuike T., Sugano S., Yamashita T., Ikeda H.
Nucleic Acids Res. 23:357-361(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
Tissue: Testis.
[2]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-417 (ISOFORMS 1/2).
Strain: C57BL/6J.
Tissue: Embryo, Eye, Forelimb, Lung and Pituitary.
[3]"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).
Strain: C57BL/6 and Czech II.
Tissue: Brain and Mammary gland.
[4]"Large-scale phosphorylation analysis of mouse liver."
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-448; SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[5]"Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis."
Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.
J. Proteome Res. 7:3957-3967(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[6]"The phagosomal proteome in interferon-gamma-activated macrophages."
Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-448; SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry."
Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.
Mol. Cell. Proteomics 8:904-912(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic fibroblast.
[8]"SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-286, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic fibroblast.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D38517 mRNA. Translation: BAA07524.1.
AK004800 mRNA. Translation: BAB23573.1.
AK031247 mRNA. Translation: BAC27318.1.
AK053643 mRNA. Translation: BAC35458.1.
AK133654 mRNA. Translation: BAE21766.1.
AK167019 mRNA. Translation: BAE39193.1.
AK168037 mRNA. Translation: BAE40020.1.
BC004028 mRNA. Translation: AAH04028.1. Different initiation.
BC054743 mRNA. Translation: AAH54743.1.
PIRI49635.
RefSeqNP_036047.2. NM_011917.2.
UniGeneMm.3065.

3D structure databases

ProteinModelPortalQ9DBR1.
SMRQ9DBR1. Positions 1-793.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid204910. 1 interaction.
IntActQ9DBR1. 3 interactions.
MINTMINT-4140454.
STRING10090.ENSMUSP00000028921.

PTM databases

PhosphoSiteQ9DBR1.

Proteomic databases

PaxDbQ9DBR1.
PRIDEQ9DBR1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000028921; ENSMUSP00000028921; ENSMUSG00000027433. [Q9DBR1-1]
GeneID24128.
KEGGmmu:24128.
UCSCuc008msq.1. mouse. [Q9DBR1-2]
uc008msr.1. mouse. [Q9DBR1-1]

Organism-specific databases

CTD22803.
MGIMGI:894687. Xrn2.

Phylogenomic databases

eggNOGCOG5049.
GeneTreeENSGT00670000098098.
HOGENOMHOG000205514.
HOVERGENHBG036677.
InParanoidQ9DBR1.
KOK12619.
OMANGEEMDN.
OrthoDBEOG7S7SCW.
PhylomeDBQ9DBR1.
TreeFamTF105977.

Enzyme and pathway databases

ReactomeREACT_93132. Metabolism of proteins.

Gene expression databases

BgeeQ9DBR1.
CleanExMM_XRN2.
GenevestigatorQ9DBR1.

Family and domain databases

InterProIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2.
IPR004859. Put_53exo.
IPR001878. Znf_CCHC.
[Graphical view]
PANTHERPTHR12341. PTHR12341. 1 hit.
PfamPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFPIRSF037239. Exonuclease_Xrn2. 1 hit.
SMARTSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSXRN2. mouse.
NextBio304163.
PROQ9DBR1.
SOURCESearch...

Entry information

Entry nameXRN2_MOUSE
AccessionPrimary (citable) accession number: Q9DBR1
Secondary accession number(s): Q3TI26 expand/collapse secondary AC list , Q3TKF2, Q3UZT9, Q61489, Q99KS7
Entry history
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: June 1, 2001
Last modified: April 16, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot