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Protein

Endoribonuclease Dicer

Gene

dicer1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. Cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. SiRNAs and miRNAs serve as guide to direct the RNA-induced silencing complex (RISC) to complementary RNAs to degrade them or prevent their translation. Gene silencing mediated by siRNAs, also called RNA interference, controls the elimination of transcripts from mobile and repetitive DNA elements of the genome but also the degradation of exogenous RNA of viral origin for instance. The miRNA pathway on the other side is a mean to specifically regulate the expression of target genes (By similarity).By similarity

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1298 – 12981Magnesium or manganese 1By similarity
Metal bindingi1377 – 13771Magnesium or manganese 1By similarity
Metal bindingi1380 – 13801Magnesium or manganese 1By similarity
Metal bindingi1648 – 16481Magnesium or manganese 2By similarity
Sitei1749 – 17491Important for activityBy similarity
Metal bindingi1753 – 17531Magnesium or manganese 2By similarity
Metal bindingi1756 – 17561Magnesium or manganese 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi54 – 618ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • gene silencing by miRNA Source: ZFIN
  • mRNA cleavage involved in gene silencing by miRNA Source: ZFIN
  • pre-miRNA processing Source: UniProtKB
  • production of miRNAs involved in gene silencing by miRNA Source: ZFIN
  • production of siRNA involved in RNA interference Source: UniProtKB
  • regulation of neurogenesis Source: ZFIN
  • targeting of mRNA for destruction involved in RNA interference Source: UniProtKB
  • ventricular system development Source: ZFIN
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

RNA-mediated gene silencing

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-DRE-203927. MicroRNA (miRNA) biogenesis.
R-DRE-426486. Small interfering RNA (siRNA) biogenesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease Dicer (EC:3.1.26.3)
Gene namesi
Name:dicer1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 17

Organism-specific databases

ZFINiZDB-GENE-030131-3445. dicer1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 18651865Endoribonuclease DicerPRO_0000373985Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6TV19.

Expressioni

Gene expression databases

BgeeiQ6TV19.

Interactioni

Subunit structurei

Component of the RISC loading complex (RLC), or micro-RNA (miRNA) loading complex (miRLC), which is composed of dicer1, ago2 and tarbp2; dicer1 and tarbp2 are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto ago2. Note that the trimeric RLC/miRLC is also referred to as RISC (By similarity).By similarity

Protein-protein interaction databases

STRINGi7955.ENSDARP00000045880.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini41 – 213173Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini419 – 588170Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini616 – 70893Dicer dsRNA-binding foldPROSITE-ProRule annotationAdd
BLAST
Domaini877 – 1028152PAZPROSITE-ProRule annotationAdd
BLAST
Domaini1262 – 1385124RNase III 1PROSITE-ProRule annotationAdd
BLAST
Domaini1609 – 1767159RNase III 2PROSITE-ProRule annotationAdd
BLAST
Domaini1792 – 185766DRBMPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi161 – 1644DECH box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1394 – 14029Poly-Asp

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.PROSITE-ProRule annotation
Contains 1 Dicer dsRNA-binding fold domain.PROSITE-ProRule annotation
Contains 1 DRBM (double-stranded RNA-binding) domain.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 PAZ domain.PROSITE-ProRule annotation
Contains 2 RNase III domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
GeneTreeiENSGT00510000046789.
HOGENOMiHOG000001567.
InParanoidiQ6TV19.
KOiK11592.
OrthoDBiEOG78PV82.
PhylomeDBiQ6TV19.
TreeFamiTF330258.

Family and domain databases

Gene3Di1.10.1520.10. 4 hits.
3.30.160.20. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_dom.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF03368. Dicer_dimer. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF04851. ResIII. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00358. DSRM. 1 hit.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 3 hits.
SSF69065. SSF69065. 4 hits.
PROSITEiPS51327. DICER_DSRBF. 1 hit.
PS50137. DS_RBD. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50821. PAZ. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6TV19-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGLQLVTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALEHNT
60 70 80 90 100
IVCLNTGSGK TFIAVLLIKE LSHQIRGENG KRTVFLVNAA SSVAQQASTV
110 120 130 140 150
RTHSDLQVGD YMSEDMTSWP EEMWNREMIE NQVLVMTCHI FLHVLKNGVL
160 170 180 190 200
PLSKINLLVF DECHLAITGH PYREIMKICE GCPSCPRILG LTASILNGKC
210 220 230 240 250
DPCDLEEKIQ NLEKILQSNA ETATDLVVLD RYASQPREEV LDCGQYQDQS
260 270 280 290 300
GLSERLLNEL DEALNFLNDC NLSVHREDRD PTFISKQVLN DCRAVLTVLG
310 320 330 340 350
PWCADKAAGI MVRELQKYIK HEQEELNRKF LLFTDTILRK IHALCEEHFS
360 370 380 390 400
PASLDLKFVT PKVIRLLEIL HEYKPFERQQ FESVEWYNNR NQDNYVSWSD
410 420 430 440 450
SEDDDEDEEA EAKEKTEANF PSPFTNILCG IIFVERRYTA VVLNRLIKEA
460 470 480 490 500
GKQDPELAYI SSNFITGHSI GKNQPRNKQM EVEFRKQEEV LRKFRAHETN
510 520 530 540 550
LLIATSIVEE GVDIPKCNLV VRFDLPTEYR SYVQSKGRAR APVSNYIMLA
560 570 580 590 600
DSERTKTFQE DLKTYKAIEK ILRNKCSKSA ECNDFELEPV TDDDNVLPPY
610 620 630 640 650
VLRSEDGGPR VTMNTAIGHV NRYCARLPSD PFTHLAPKCK TVEMNTGGYR
660 670 680 690 700
STLFLPINSP LRVPVTGPVM NCARLAEKAV ALLCCEKLHK IGELDDHLMP
710 720 730 740 750
VGKETVKYEE ELDLHDEEET SVPGRPGSTK RRQCSPKAIP ECLRGCYPVP
760 770 780 790 800
EQPCYLYVIG MVLTTPLPDE LNFRRRKLYP PEDTTRCFGI LTAKPIPRIP
810 820 830 840 850
HFPVYTRSGE VTISIELQKS GFSLSAEQLE LITRLHQYIF SHILRLEKPA
860 870 880 890 900
LEFKPVEADS AYCVLPLNIV EDSNTLDLDF KFMEDIEKSE ARIGIPNTQY
910 920 930 940 950
TKQNPFIFKL EDYQDAVIIP RYRNFDQPHR FYVADVYTDL TPLSKFPSPE
960 970 980 990 1000
YETFAEYYKT KYNLDLSNVN QPLLDVDHTS SRLNLLTPRH LNQKGKALPL
1010 1020 1030 1040 1050
SSAEKRKAKW ESLQNKQILV PELCAIHPIP ASLWRKAVCL PSILYRLHCL
1060 1070 1080 1090 1100
LTAEELRSQT AIDAGVGAQT LPPDFRYPNL DFGWKKSIDS KSFISCPSAC
1110 1120 1130 1140 1150
MEEDDDHCKL GTSSDSNHTA PESCSMEVSQ PPEGAPNTPD EKLETLTLPV
1160 1170 1180 1190 1200
TDLNKDCFPN LPNGTQADSD DLPHRSDVCQ CSQLGPLERD LSTQTTTSVS
1210 1220 1230 1240 1250
VRPSPAGEPQ PWPSDECTGR SSDLCDPHVK KPTSKHCPKS ETATSTPAPS
1260 1270 1280 1290 1300
ETSSEDCRSA CAGPAWDSPK TLGPNPGLIL QALTLSNASD GFNLERLEML
1310 1320 1330 1340 1350
GDSFLKHAIT TYLFCTYPDA HEGRLSYMRS KKVSNCNLYR LGKKKGLPSR
1360 1370 1380 1390 1400
MVVSIFDPPV NWLPPGYVVN QDKSSTDKWD SDENKDLANG KASDDEDEDD
1410 1420 1430 1440 1450
DDEPEEAEVE PSKEDVNVED DLEYYYEHIR FIDSMLIGSG AFGKKISLQP
1460 1470 1480 1490 1500
TDPGYEWKAP KKAHNSHFSP DGGADEFDYS SWDAMCYLDP SKAGEEDDFV
1510 1520 1530 1540 1550
VGFWNPSEEN CGTDIGKQSI SYDLHTEQCI ADKSIADCVE ALLGCYLTSC
1560 1570 1580 1590 1600
GERAAQLFLC SLGLKVLPPE KQSSGGSAEL QYGWLKIPPR CMFEHPDAER
1610 1620 1630 1640 1650
TLNHLISGFL NFESKINYTF KNKAYLLQAF THASYHYNTI TDCYQRLEFL
1660 1670 1680 1690 1700
GDAILDYLIT KHLYEDPRQH SPGVLTDLRS ALVNNTIFAS LAVKYDYHKY
1710 1720 1730 1740 1750
FKAVSPELFH VIDDFVQFQL EKNEMQGMDS ELRRSEEDEE KEEDIEVPKA
1760 1770 1780 1790 1800
MGDIFESLAG AIYMDSGMSL ETVWQVYYPM MRPLIEKFSA NVPRSPVREL
1810 1820 1830 1840 1850
LEMEPETAKF SPAERTYDGK VRVTVEVVGK GKFKGVGRSY RIAKSAAARR
1860
ALRSLKANQP QVQNN
Length:1,865
Mass (Da):210,817
Last modified:May 5, 2009 - v2
Checksum:i55B1700E719B2007
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti739 – 75113IPECL…YPVPE → VK in AAQ90464 (PubMed:14528306).CuratedAdd
BLAST
Sequence conflicti921 – 9211R → K in AAQ90464 (PubMed:14528306).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL772219 Genomic DNA. No translation available.
AY386319 mRNA. Translation: AAQ90464.1.
RefSeqiNP_001154925.1. NM_001161453.2.
XP_005158722.1. XM_005158665.2.
XP_005158723.1. XM_005158666.2.
XP_009291240.1. XM_009292965.1.
UniGeneiDr.78137.

Genome annotation databases

EnsembliENSDART00000045881; ENSDARP00000045880; ENSDARG00000001129.
ENSDART00000109826; ENSDARP00000100328; ENSDARG00000001129.
GeneIDi324724.
KEGGidre:324724.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL772219 Genomic DNA. No translation available.
AY386319 mRNA. Translation: AAQ90464.1.
RefSeqiNP_001154925.1. NM_001161453.2.
XP_005158722.1. XM_005158665.2.
XP_005158723.1. XM_005158666.2.
XP_009291240.1. XM_009292965.1.
UniGeneiDr.78137.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000045880.

Proteomic databases

PaxDbiQ6TV19.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000045881; ENSDARP00000045880; ENSDARG00000001129.
ENSDART00000109826; ENSDARP00000100328; ENSDARG00000001129.
GeneIDi324724.
KEGGidre:324724.

Organism-specific databases

CTDi23405.
ZFINiZDB-GENE-030131-3445. dicer1.

Phylogenomic databases

eggNOGiKOG0701. Eukaryota.
COG0571. LUCA.
COG1111. LUCA.
GeneTreeiENSGT00510000046789.
HOGENOMiHOG000001567.
InParanoidiQ6TV19.
KOiK11592.
OrthoDBiEOG78PV82.
PhylomeDBiQ6TV19.
TreeFamiTF330258.

Enzyme and pathway databases

ReactomeiR-DRE-203927. MicroRNA (miRNA) biogenesis.
R-DRE-426486. Small interfering RNA (siRNA) biogenesis.

Miscellaneous databases

PROiQ6TV19.

Gene expression databases

BgeeiQ6TV19.

Family and domain databases

Gene3Di1.10.1520.10. 4 hits.
3.30.160.20. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR005034. Dicer_dimerisation_dom.
IPR014720. dsRBD_dom.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR003100. PAZ_dom.
IPR000999. RNase_III_dom.
[Graphical view]
PfamiPF03368. Dicer_dimer. 1 hit.
PF00271. Helicase_C. 1 hit.
PF02170. PAZ. 1 hit.
PF04851. ResIII. 1 hit.
PF00636. Ribonuclease_3. 2 hits.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00358. DSRM. 1 hit.
SM00490. HELICc. 1 hit.
SM00949. PAZ. 1 hit.
SM00535. RIBOc. 2 hits.
[Graphical view]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF52540. SSF52540. 3 hits.
SSF69065. SSF69065. 4 hits.
PROSITEiPS51327. DICER_DSRBF. 1 hit.
PS50137. DS_RBD. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50821. PAZ. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. "The microRNA-producing enzyme Dicer1 is essential for zebrafish development."
    Wienholds E., Koudijs M.J., van Eeden F.J.M., Cuppen E., Plasterk R.H.A.
    Nat. Genet. 35:217-218(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 612-1865.

Entry informationi

Entry nameiDICER_DANRE
AccessioniPrimary (citable) accession number: Q6TV19
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 5, 2009
Last sequence update: May 5, 2009
Last modified: June 8, 2016
This is version 80 of the entry and version 2 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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.