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Q9Y3B8

- ORN_HUMAN

UniProt

Q9Y3B8 - ORN_HUMAN

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Protein
Oligoribonuclease, mitochondrial
Gene
REXO2, SFN, SMFN, CGI-114
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 1641 Reviewed prediction

GO - Molecular functioni

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

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
Complete GO annotation...

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

Isoform 1 : Mitochondrion intermembrane space. Mitochondrion matrix 1 Publication
Isoform 2 : Nucleus 1 Publication
Isoform 3 : Cytoplasm 1 Publication

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
Complete GO annotation...

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 – 2525Mitochondrion Reviewed prediction
Add
BLAST
Chaini26 – 237212Oligoribonuclease, mitochondrialUniRule annotation
PRO_0000020273Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei122 – 1221Phosphotyrosine1 Publication
Modified residuei173 – 1731N6-acetyllysine By 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 Inferred.

Protein-protein interaction databases

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

Structurei

3D structure databases

ProteinModelPortaliQ9Y3B8.
SMRiQ9Y3B8. Positions 41-216.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Belongs to the oligoribonuclease family.
Contains 1 exonuclease domain.

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 3838Missing in isoform 2.
VSP_003775Add
BLAST
Alternative sequencei1 – 3232Missing in isoform 3.
VSP_054954Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti103 – 1031K → R in CAB53690. 1 Publication
Sequence conflicti103 – 1031K → R in CAG38531. 1 Publication

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...

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 128 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

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