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Q9DBR1

- XRN2_MOUSE

UniProt

Q9DBR1 - XRN2_MOUSE

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Protein

5'-3' exoribonuclease 2

Gene
Xrn2, Dhm1
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri262 – 27817CCHC-typeAdd
BLAST

GO - Molecular functioni

  1. 5'-3' exonuclease activity Source: UniProtKB
  2. 5'-3' exoribonuclease activity Source: UniProtKB
  3. nucleic acid binding Source: InterPro
  4. protein binding Source: MGI
  5. zinc ion binding Source: InterPro

GO - Biological processi

  1. cell growth Source: UniProtKB
  2. DNA catabolic process, exonucleolytic Source: UniProtKB
  3. DNA recombination Source: UniProtKB
  4. DNA repair Source: UniProtKB
  5. DNA-templated transcription, termination Source: UniProtKB-KW
  6. microtubule-based process Source: UniProtKB
  7. mRNA processing Source: UniProtKB-KW
  8. regulation of transcription, DNA-templated Source: UniProtKB-KW
  9. RNA metabolic process Source: UniProtKB
  10. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
  11. spermatogenesis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, Transcription, Transcription regulation, Transcription termination

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
5'-3' exoribonuclease 2 (EC:3.1.13.-)
Alternative name(s):
Protein Dhm1
Gene namesi
Name:Xrn2
Synonyms:Dhm1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 2

Organism-specific databases

MGIiMGI:894687. Xrn2.

Subcellular locationi

Nucleusnucleolus By similarity

GO - Cellular componenti

  1. aggresome Source: Ensembl
  2. nucleolus Source: UniProtKB
  3. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9519515'-3' exoribonuclease 2PRO_0000071397Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei286 – 2861N6-acetyllysine1 Publication
Modified residuei439 – 4391Phosphothreonine By similarity
Modified residuei448 – 4481Phosphoserine2 Publications
Modified residuei471 – 4711Phosphoserine By similarity
Modified residuei473 – 4731Phosphoserine By similarity
Modified residuei475 – 4751Phosphoserine By similarity
Modified residuei499 – 4991Phosphoserine3 Publications
Modified residuei501 – 5011Phosphoserine3 Publications

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9DBR1.
PaxDbiQ9DBR1.
PRIDEiQ9DBR1.

PTM databases

PhosphoSiteiQ9DBR1.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiQ9DBR1.
CleanExiMM_XRN2.
GenevestigatoriQ9DBR1.

Interactioni

Protein-protein interaction databases

BioGridi204910. 2 interactions.
IntActiQ9DBR1. 3 interactions.
MINTiMINT-4140454.
STRINGi10090.ENSMUSP00000028921.

Structurei

3D structure databases

ProteinModelPortaliQ9DBR1.
SMRiQ9DBR1. Positions 1-430, 502-785.

Family & Domainsi

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri262 – 27817CCHC-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5049.
GeneTreeiENSGT00670000098098.
HOGENOMiHOG000205514.
HOVERGENiHBG036677.
InParanoidiQ9DBR1.
KOiK12619.
OMAiMMVEIFK.
OrthoDBiEOG7S7SCW.
PhylomeDBiQ9DBR1.
TreeFamiTF105977.

Family and domain databases

InterProiIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2.
IPR004859. Put_53exo.
IPR001878. Znf_CCHC.
[Graphical view]
PANTHERiPTHR12341. PTHR12341. 1 hit.
PfamiPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.
SMARTiSM00343. ZnF_C2HC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9DBR1-1) [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

MGVPAFFRWL SRKYPSIIVN CVEEKPKECN GVKIPVDASK PNPNDVEFDN    50
LYLDMNGIIH PCTHPEDKPA PKNEDEMMVA IFEYIDRLFN IVRPRRLLYM 100
AIDGVAPRAK MNQQRSRRFR ASKEGMEAAV EKQRVREEIL AKGGFLPPEE 150
IKERFDSNCI TPGTEFMDNL AKCLRYYIAD RLNNDPGWKN LTVILSDASA 200
PGEGEHKIMD YIRRQRAQPN HDPNTHHCLC GADADLIMLG LATHEPNFTI 250
IREEFKPNKP KPCALCNQFG HEVKDCEGLP REKKGKHDEL ADSLPCAEGE 300
FIFLRLNVLR EYLERELTMA SLPFPFDVER SIDDWVFMCF FVGNDFLPHL 350
PSLEIREGAI DRLVNIYKNV VHKTGGYLTE SGYVNLQRVQ MIMLAVGEVE 400
DSIFKKRKDD EDSFRRRQKE KRKRMKRDQP AFTPSGILTP HALGSRNSPG 450
CQVASNPRQA AYEMRMQRNS SPSISPNTSF ASDGSPSPLG GIKRKAEDSD 500
SEPEPEDNVR LWEAGWKQRY YKNKFDVDAA DEKFRRKVVQ SYVEGLCWVL 550
RYYYQGCASW KWYYPFHYAP FASDFEGIAD MSSEFEKGTK PFKPLEQLMG 600
VFPAASGNFL PPTWRKLMSD PDSSIIDFYP EDFAIDLNGK KYAWQGVALL 650
PFVDERRLRA ALEEVYPDLT PEENRRNSLG GDVLFVGKLH PLRDFILELY 700
QTGSTEPVDV PPELCHGIQG TFSLDEEAIL PDQTVCSPVP MLRDLTQNTA 750
VSINFKDPQF AEDYVFKAAM LPGARKPATV LKPGDWEKSS NGRQWKPQLG 800
FNRDRRPVHL DQAAFRTLGH VTPRGSGTSV YTNTALPPAN YQGNNYRPLL 850
RGQAQIPKLM SNMRPQDSWR GPPPLFQQHR FERSVGAEPL LPWNRMIQNQ 900
NAAFQPNQYQ MLGGPGGYPP RRDDHRGGRQ GYPREGRKYP LPPPSGRYSW 950
N 951
Length:951
Mass (Da):108,687
Last modified:June 1, 2001 - v1
Checksum:iCF57479291DD18B9
GO
Isoform 2 (identifier: Q9DBR1-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:947
Mass (Da):108,108
Checksum:iD07EDE545BB57F24
GO

Sequence cautioni

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei931 – 95121GYPRE…RYSWN → VISTMWAVEGKQHTAHC in isoform 2. VSP_007235Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti122 – 1243SKE → IKG in BAA07524. 1 Publication
Sequence conflicti221 – 2211H → Q in BAA07524. 1 Publication
Sequence conflicti306 – 3061L → P in BAE40020. 1 Publication
Sequence conflicti332 – 3321I → N in BAA07524. 1 Publication
Sequence conflicti336 – 3361V → E in BAA07524. 1 Publication
Sequence conflicti440 – 4401P → H in BAE40020. 1 Publication
Sequence conflicti449 – 4491P → Q in BAE40020. 1 Publication
Sequence conflicti493 – 4931K → R in BAA07524. 1 Publication
Sequence conflicti563 – 5631Y → L in BAA07524. 1 Publication
Sequence conflicti712 – 7121P → H in BAC27318. 1 Publication
Sequence conflicti734 – 7341T → K in BAC27318. 1 Publication
Sequence conflicti837 – 8371P → L in BAA07524. 1 Publication
Sequence conflicti866 – 8661Q → K in BAA07524. 1 Publication
Sequence conflicti889 – 8891P → H in BAC27318. 1 Publication
Sequence conflicti923 – 9231D → G in BAE40020. 1 Publication
Sequence conflicti930 – 9301Q → QV in BAC27318. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS38258.1. [Q9DBR1-1]
PIRiI49635.
RefSeqiNP_036047.2. NM_011917.2. [Q9DBR1-1]
UniGeneiMm.3065.

Genome annotation databases

EnsembliENSMUST00000028921; ENSMUSP00000028921; ENSMUSG00000027433. [Q9DBR1-1]
GeneIDi24128.
KEGGimmu:24128.
UCSCiuc008msq.1. mouse. [Q9DBR1-2]
uc008msr.1. mouse. [Q9DBR1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS38258.1. [Q9DBR1-1 ]
PIRi I49635.
RefSeqi NP_036047.2. NM_011917.2. [Q9DBR1-1 ]
UniGenei Mm.3065.

3D structure databases

ProteinModelPortali Q9DBR1.
SMRi Q9DBR1. Positions 1-430, 502-785.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 204910. 2 interactions.
IntActi Q9DBR1. 3 interactions.
MINTi MINT-4140454.
STRINGi 10090.ENSMUSP00000028921.

PTM databases

PhosphoSitei Q9DBR1.

Proteomic databases

MaxQBi Q9DBR1.
PaxDbi Q9DBR1.
PRIDEi Q9DBR1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000028921 ; ENSMUSP00000028921 ; ENSMUSG00000027433 . [Q9DBR1-1 ]
GeneIDi 24128.
KEGGi mmu:24128.
UCSCi uc008msq.1. mouse. [Q9DBR1-2 ]
uc008msr.1. mouse. [Q9DBR1-1 ]

Organism-specific databases

CTDi 22803.
MGIi MGI:894687. Xrn2.

Phylogenomic databases

eggNOGi COG5049.
GeneTreei ENSGT00670000098098.
HOGENOMi HOG000205514.
HOVERGENi HBG036677.
InParanoidi Q9DBR1.
KOi K12619.
OMAi MMVEIFK.
OrthoDBi EOG7S7SCW.
PhylomeDBi Q9DBR1.
TreeFami TF105977.

Miscellaneous databases

ChiTaRSi XRN2. mouse.
NextBioi 304163.
PROi Q9DBR1.
SOURCEi Search...

Gene expression databases

Bgeei Q9DBR1.
CleanExi MM_XRN2.
Genevestigatori Q9DBR1.

Family and domain databases

InterProi IPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2.
IPR004859. Put_53exo.
IPR001878. Znf_CCHC.
[Graphical view ]
PANTHERi PTHR12341. PTHR12341. 1 hit.
Pfami PF03159. XRN_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF037239. Exonuclease_Xrn2. 1 hit.
SMARTi SM00343. ZnF_C2HC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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.

Entry informationi

Entry nameiXRN2_MOUSE
AccessioniPrimary (citable) accession number: Q9DBR1
Secondary accession number(s): Q3TI26
, Q3TKF2, Q3UZT9, Q61489, Q99KS7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: June 1, 2001
Last modified: July 9, 2014
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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