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Q9Y3B8

- ORN_HUMAN

UniProt

Q9Y3B8 - ORN_HUMAN

Protein

Oligoribonuclease, mitochondrial

Gene

REXO2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 129 (01 Oct 2014)
      Sequence version 3 (17 Oct 2006)
      Previous versions | rss
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    Functioni

    3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.1 Publication

    Cofactori

    Manganese.

    Enzyme regulationi

    Inhibited by adenosine 3',5'-bisphosphate.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei164 – 1641Sequence Analysis

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: MGI
    2. nucleic acid binding Source: InterPro

    GO - Biological processi

    1. nucleic acid phosphodiester bond hydrolysis Source: GOC
    2. nucleobase-containing compound metabolic process Source: MGI
    3. nucleotide metabolic process Source: ProtInc

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Ligandi

    Manganese

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Oligoribonuclease, mitochondrial (EC:3.1.-.-)
    Alternative name(s):
    RNA exonuclease 2 homolog
    Small fragment nuclease
    Gene namesi
    Name:REXO2
    Synonyms:SFN, SMFN
    ORF Names:CGI-114
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 11

    Organism-specific databases

    HGNCiHGNC:17851. REXO2.

    Subcellular locationi

    GO - Cellular componenti

    1. focal adhesion Source: HPA
    2. mitochondrial intermembrane space Source: UniProtKB-SubCell
    3. mitochondrial matrix Source: UniProtKB-SubCell
    4. mitochondrion Source: HPA
    5. nucleolus Source: HPA
    6. nucleus Source: LIFEdb

    Keywords - Cellular componenti

    Cytoplasm, Mitochondrion, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi168 – 1681D → A: Abolishes activity.

    Organism-specific databases

    PharmGKBiPA142671085.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 2525MitochondrionSequence AnalysisAdd
    BLAST
    Chaini26 – 237212Oligoribonuclease, mitochondrialPRO_0000020273Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei122 – 1221Phosphotyrosine1 Publication
    Modified residuei173 – 1731N6-acetyllysineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9Y3B8.
    PaxDbiQ9Y3B8.
    PRIDEiQ9Y3B8.

    PTM databases

    PhosphoSiteiQ9Y3B8.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9Y3B8.
    BgeeiQ9Y3B8.
    CleanExiHS_REXO2.
    HS_SFN.
    GenevestigatoriQ9Y3B8.

    Organism-specific databases

    HPAiHPA038450.
    HPA038451.

    Interactioni

    Subunit structurei

    Homotetramer.Curated

    Protein-protein interaction databases

    BioGridi117473. 2 interactions.
    MINTiMINT-3085757.
    STRINGi9606.ENSP00000265881.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Y3B8.
    SMRiQ9Y3B8. Positions 41-216.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini43 – 207165ExonucleaseAdd
    BLAST

    Sequence similaritiesi

    Belongs to the oligoribonuclease family.Curated
    Contains 1 exonuclease domain.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG1949.
    HOGENOMiHOG000246596.
    HOVERGENiHBG002323.
    InParanoidiQ9Y3B8.
    KOiK13288.
    OMAiALEAYFH.
    OrthoDBiEOG7J4483.
    PhylomeDBiQ9Y3B8.
    TreeFamiTF314084.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    HAMAPiMF_00045. Oligoribonuclease.
    InterProiIPR006055. Exonuclease.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR022894. Oligoribonuclease.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF00929. RNase_T. 1 hit.
    [Graphical view]
    SMARTiSM00479. EXOIII. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.

    Sequences (3)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 3 isoformsi produced by alternative initiation. Align

    Isoform 1 (identifier: Q9Y3B8-1) [UniParc]FASTAAdd to Basket

    Also known as: Sfn-alpha

    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

    MLGGSLGSRL LRGVGGSHGR FGARGVREGG AAMAAGESMA QRMVWVDLEM    50
    TGLDIEKDQI IEMACLITDS DLNILAEGPN LIIKQPDELL DSMSDWCKEH 100
    HGKSGLTKAV KESTITLQQA EYEFLSFVRQ QTPPGLCPLA GNSVHEDKKF 150
    LDKYMPQFMK HLHYRIIDVS TVKELCRRWY PEEYEFAPKK AASHRALDDI 200
    SESIKELQFY RNNIFKKKID EKKRKIIENG ENEKTVS 237
    Length:237
    Mass (Da):26,833
    Last modified:October 17, 2006 - v3
    Checksum:iA0343A8918B11B82
    GO
    Isoform 2 (identifier: Q9Y3B8-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-38: Missing.

    Show »
    Length:199
    Mass (Da):23,208
    Checksum:iE96469443EFF140A
    GO
    Isoform 3 (identifier: Q9Y3B8-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-32: Missing.

    Show »
    Length:205
    Mass (Da):23,754
    Checksum:i77C526551A46BEFC
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti103 – 1031K → R in CAB53690. (PubMed:11230166)Curated
    Sequence conflicti103 – 1031K → R in CAG38531. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 3838Missing in isoform 2. 1 PublicationVSP_003775Add
    BLAST
    Alternative sequencei1 – 3232Missing in isoform 3. CuratedVSP_054954Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF151872 mRNA. Translation: AAD34109.1.
    AL110239 mRNA. Translation: CAB53690.1.
    AK312042 mRNA. Translation: BAG34979.1.
    CR533500 mRNA. Translation: CAG38531.1.
    AK223200 mRNA. Translation: BAD96920.1.
    CH471065 Genomic DNA. Translation: EAW67250.1.
    BC105024 mRNA. Translation: AAI05025.1.
    BC105026 mRNA. Translation: AAI05027.1.
    BC107887 mRNA. Translation: AAI07888.1.
    BC143701 mRNA. Translation: AAI43702.1.
    CCDSiCCDS8371.1. [Q9Y3B8-1]
    PIRiT14770.
    RefSeqiNP_056338.2. NM_015523.3. [Q9Y3B8-1]
    UniGeneiHs.677190.
    Hs.714231.

    Genome annotation databases

    EnsembliENST00000265881; ENSP00000265881; ENSG00000076043. [Q9Y3B8-1]
    GeneIDi25996.
    KEGGihsa:25996.
    UCSCiuc001poy.3. human. [Q9Y3B8-1]

    Polymorphism databases

    DMDMi116242694.

    Keywords - Coding sequence diversityi

    Alternative initiation

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF151872 mRNA. Translation: AAD34109.1 .
    AL110239 mRNA. Translation: CAB53690.1 .
    AK312042 mRNA. Translation: BAG34979.1 .
    CR533500 mRNA. Translation: CAG38531.1 .
    AK223200 mRNA. Translation: BAD96920.1 .
    CH471065 Genomic DNA. Translation: EAW67250.1 .
    BC105024 mRNA. Translation: AAI05025.1 .
    BC105026 mRNA. Translation: AAI05027.1 .
    BC107887 mRNA. Translation: AAI07888.1 .
    BC143701 mRNA. Translation: AAI43702.1 .
    CCDSi CCDS8371.1. [Q9Y3B8-1 ]
    PIRi T14770.
    RefSeqi NP_056338.2. NM_015523.3. [Q9Y3B8-1 ]
    UniGenei Hs.677190.
    Hs.714231.

    3D structure databases

    ProteinModelPortali Q9Y3B8.
    SMRi Q9Y3B8. Positions 41-216.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 117473. 2 interactions.
    MINTi MINT-3085757.
    STRINGi 9606.ENSP00000265881.

    PTM databases

    PhosphoSitei Q9Y3B8.

    Polymorphism databases

    DMDMi 116242694.

    Proteomic databases

    MaxQBi Q9Y3B8.
    PaxDbi Q9Y3B8.
    PRIDEi Q9Y3B8.

    Protocols and materials databases

    DNASUi 25996.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000265881 ; ENSP00000265881 ; ENSG00000076043 . [Q9Y3B8-1 ]
    GeneIDi 25996.
    KEGGi hsa:25996.
    UCSCi uc001poy.3. human. [Q9Y3B8-1 ]

    Organism-specific databases

    CTDi 25996.
    GeneCardsi GC11P114311.
    H-InvDB HIX0010145.
    HGNCi HGNC:17851. REXO2.
    HPAi HPA038450.
    HPA038451.
    MIMi 607149. gene.
    neXtProti NX_Q9Y3B8.
    PharmGKBi PA142671085.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1949.
    HOGENOMi HOG000246596.
    HOVERGENi HBG002323.
    InParanoidi Q9Y3B8.
    KOi K13288.
    OMAi ALEAYFH.
    OrthoDBi EOG7J4483.
    PhylomeDBi Q9Y3B8.
    TreeFami TF314084.

    Miscellaneous databases

    ChiTaRSi REXO2. human.
    GeneWikii REXO2.
    GenomeRNAii 25996.
    NextBioi 47710.
    PROi Q9Y3B8.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Y3B8.
    Bgeei Q9Y3B8.
    CleanExi HS_REXO2.
    HS_SFN.
    Genevestigatori Q9Y3B8.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    HAMAPi MF_00045. Oligoribonuclease.
    InterProi IPR006055. Exonuclease.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR022894. Oligoribonuclease.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF00929. RNase_T. 1 hit.
    [Graphical view ]
    SMARTi SM00479. EXOIII. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics."
      Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.
      Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Kidney.
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Skeletal muscle.
    4. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    5. Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
      Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Kidney proximal tubule.
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    7. "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).
      Tissue: Brain and Placenta.
    8. "The human homolog of Escherichia coli Orn degrades small single-stranded RNA and DNA oligomers."
      Nguyen L.H., Erzberger J.P., Root J., Wilson D.M. III
      J. Biol. Chem. 275:25900-25906(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    9. "Immunoaffinity profiling of tyrosine phosphorylation in cancer cells."
      Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J.
      Nat. Biotechnol. 23:94-101(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-122, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells."
      Mechold U., Ogryzko V., Ngo S., Danchin A.
      Nucleic Acids Res. 34:2364-2373(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.
    11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. Cited for: FUNCTION, SUBCELLULAR LOCATION, MISCELLANEOUS, ALTERNATIVE INITIATION (ISOFORM 3).

    Entry informationi

    Entry nameiORN_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y3B8
    Secondary accession number(s): B2R532
    , Q32Q18, Q53FT1, Q6FIC6, Q9UFY7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: October 17, 2006
    Last modified: October 1, 2014
    This is version 129 of the entry and version 3 of the sequence. [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

    Miscellaneous

    Depletion of REXO2 by RNA interference causes a strong morphological phenotype showing disorganized network of punctate and granular mitochondria. Lack of REXO2 protein also causes a substantial decrease of mitochondrial nucleic acid content and impaired de novo mitochondrial protein synthesis.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 11
      Human chromosome 11: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3