ID A0A0R4IHL6_DANRE Unreviewed; 647 AA.
AC A0A0R4IHL6; A0A8N7V031;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 27-MAR-2024, entry version 50.
DE RecName: Full=Poly(A)-specific ribonuclease PARN {ECO:0000256|ARBA:ARBA00015918};
DE EC=3.1.13.4 {ECO:0000256|ARBA:ARBA00012161};
DE AltName: Full=Polyadenylate-specific ribonuclease {ECO:0000256|ARBA:ARBA00031923};
GN Name=parn {ECO:0000313|Ensembl:ENSDARP00000133177,
GN ECO:0000313|RefSeq:NP_957382.2, ECO:0000313|ZFIN:ZDB-GENE-040426-880};
GN Synonyms=zgc:56067 {ECO:0000313|RefSeq:NP_957382.2};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000313|Ensembl:ENSDARP00000133177};
RN [1] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=15520368; DOI=10.1073/pnas.0407241101;
RA Song H.D., Sun X.J., Deng M., Zhang G.W., Zhou Y., Wu X.Y., Sheng Y.,
RA Chen Y., Ruan Z., Jiang C.L., Fan H.Y., Zon L.I., Kanki J.P., Liu T.X.,
RA Look A.T., Chen Z.;
RT "Hematopoietic gene expression profile in zebrafish kidney marrow.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:16240-16245(2004).
RN [2] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=17895525;
RA Wang H., Zhou Q., Kesinger J.W., Norris C., Valdez C.;
RT "Heme regulates exocrine peptidase precursor genes in zebrafish.";
RL Exp. Biol. Med. (Maywood) 232:1170-1180(2007).
RN [3] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=18307296; DOI=10.1021/pr700667w;
RA Lemeer S., Pinkse M.W., Mohammed S., van Breukelen B., den Hertog J.,
RA Slijper M., Heck A.J.;
RT "Online automated in vivo zebrafish phosphoproteomics: from large-scale
RT analysis down to a single embryo.";
RL J. Proteome Res. 7:1555-1564(2008).
RN [4] {ECO:0000313|Ensembl:ENSDARP00000133177, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000133177};
RX PubMed=23594743; DOI=10.1038/nature12111;
RG Genome Reference Consortium Zebrafish;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Eliott D.,
RA Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Mortimer B.,
RA Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M.,
RA Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M.,
RA Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J.,
RA Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D.,
RA Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K.,
RA Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R.,
RA Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M.,
RA Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D.,
RA Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M.,
RA Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M.,
RA Woodmansey R., Clark G., Cooper J., Cooper J., Tromans A., Grafham D.,
RA Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J.,
RA Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I.,
RA Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G., Osoegawa K., Zhu B.,
RA Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P.,
RA Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R.,
RA Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I.,
RA Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H.,
RA Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [5] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=26342108;
RA Dhanraj S., Gunja S.M., Deveau A.P., Nissbeck M., Boonyawat B.,
RA Coombs A.J., Renieri A., Mucciolo M., Marozza A., Buoni S., Turner L.,
RA Li H., Jarrar A., Sabanayagam M., Kirby M., Shago M., Pinto D.,
RA Berman J.N., Scherer S.W., Virtanen A., Dror Y.;
RT "Bone marrow failure and developmental delay caused by mutations in
RT poly(A)-specific ribonuclease (PARN).";
RL J. Med. Genet. 52:738-748(2015).
RN [6] {ECO:0000313|Ensembl:ENSDARP00000133177}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000133177};
RG Ensembl;
RL Submitted (NOV-2015) to UniProtKB.
RN [7] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=27235108; DOI=10.1016/j.bbrc.2016.05.074;
RA Du Z., Chen X., Li X., He K., Ji S., Shi W., Hao A.;
RT "Protein palmitoylation activate zygotic gene expression during the
RT maternal-to-zygotic transition.";
RL Biochem. Biophys. Res. Commun. 475:194-201(2016).
RN [8] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=26566657;
RA Lin C.L., Taggart A.J., Lim K.H., Cygan K.J., Ferraris L., Creton R.,
RA Huang Y.T., Fairbrother W.G.;
RT "RNA structure replaces the need for U2AF2 in splicing.";
RL Genome Res. 26:12-23(2016).
RN [9] {ECO:0000313|RefSeq:NP_957382.2}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RX PubMed=30061596;
RA Beaudoin J.D., Novoa E.M., Vejnar C.E., Yartseva V., Takacs C.M.,
RA Kellis M., Giraldez A.J.;
RT "Analyses of mRNA structure dynamics identify embryonic gene regulatory
RT programs.";
RL Nat. Struct. Mol. Biol. 25:677-686(2018).
RN [10] {ECO:0000313|RefSeq:NP_957382.2}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_957382.2};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC Evidence={ECO:0000256|ARBA:ARBA00001663};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496}.
CC Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the CAF1 family.
CC {ECO:0000256|ARBA:ARBA00008372}.
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DR EMBL; CU550701; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_957382.2; NM_201088.2.
DR Ensembl; ENSDART00000160658; ENSDARP00000133177; ENSDARG00000102634.
DR Ensembl; ENSDART00000160658.2; ENSDARP00000133177.1; ENSDARG00000102634.2.
DR GeneID; 791461; -.
DR AGR; ZFIN:ZDB-GENE-040426-880; -.
DR CTD; 5073; -.
DR ZFIN; ZDB-GENE-040426-880; parn.
DR OrthoDB; 276176at2759; -.
DR Proteomes; UP000000437; Chromosome 1.
DR Bgee; ENSDARG00000102634; Expressed in cleaving embryo and 30 other cell types or tissues.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:InterPro.
DR CDD; cd02637; R3H_PARN; 1.
DR CDD; cd12428; RRM_PARN; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 2.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR034042; PARN_R3H.
DR InterPro; IPR014789; PolyA-riboNase_RNA-binding.
DR InterPro; IPR001374; R3H_dom.
DR InterPro; IPR036867; R3H_dom_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR PANTHER; PTHR15092; POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1; 1.
DR PANTHER; PTHR15092:SF44; POLY(A)-SPECIFIC RIBONUCLEASE PARN; 1.
DR Pfam; PF04857; CAF1; 1.
DR Pfam; PF08675; RNA_bind; 1.
DR SUPFAM; SSF82708; R3H domain; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR SUPFAM; SSF54928; RNA-binding domain, RBD; 1.
DR PROSITE; PS51061; R3H; 1.
PE 1: Evidence at protein level;
KW Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Proteomics identification {ECO:0007829|PeptideAtlas:A0A0R4IHL6};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437}.
FT DOMAIN 177..243
FT /note="R3H"
FT /evidence="ECO:0000259|PROSITE:PS51061"
FT REGION 606..647
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 624..638
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 647 AA; 73669 MW; EBB8EE58A3113A8C CRC64;
MEVTRQNFKE ILPEVCNAVQ EADFISIDGE FTGISDGPSV SALTNGLDTP EERYTKLRKH
SMNFLLFQFG VCTFRYDQNQ STYITKAFNF YIFPKPFSRT SPDIKFICQS SSIDFLASQG
FDFNKVFRSG IPYLTQEEEC QLREQYEERR GQMNGAGPVS YTPPSGTGVC NVPEDQREFI
RSVEEKVEAL LKNTDQTLDL EPCTGFQRKL IYQTLNSKYS KGLHVETLET EKKERFIQIS
KVDDEERRRR EQQKQQREQE ELNDAVGFSR VIRAISKSGK LVVGHNMLLD VMHTIHQFCG
PLPEELDDFK EVAMTVFPRL LDTKLMASTQ PFKEIIHNTS LAELHKQLRQ KPFRPPTTEC
PEGLQSYDTS TEQLHEAGYD AFITGLCFIS MANYLGSFLT PPKSHISARS KLLEPFYNKL
FLMRVIDIPY LNMSGPDLQP KRDHVLYVTF PKEWKTSDLY QLFSAFGNIQ VSWVDDTSAF
VSLSQTEQVQ IAMNTSRYAE SYRIQTYAEY LQSRQKNTHS SRKWASDGWA DTSYPSVAMT
TASGYSHTDN RHQAVKRSIS PSLDEQNHGA DSSWTNYSVK KIKTEGSCTQ TYADVAGSCD
WPRLQADEGG ASVSPVAEEA ELDEFSANQS QASETTPPAL FDVPQVW
//
