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2024-11-01 12:49:05, GGRNA.v2 : RefSeq release 226 (Sep, 2024)

LOCUS       XM_021467114            9664 bp    mRNA    linear   VRT 08-SEP-2024
DEFINITION  PREDICTED: Danio rerio dicer 1, ribonuclease type III (dicer1),
            transcript variant X4, mRNA.
ACCESSION   XM_021467114
VERSION     XM_021467114.2
DBLINK      BioProject: PRJNA13922
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_007128.7) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Sep 8, 2024 this sequence version replaced XM_021467114.1.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_000002035.6-RS_2024_08
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.3
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 08/15/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..9664
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="17"
     gene            1..9664
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="dicer 1, ribonuclease type III; Derived by
                     automated computational analysis using gene prediction
                     method: Gnomon. Supporting evidence includes similarity
                     to: 2 mRNAs, 10 ESTs, 669 long SRA reads, 19 Proteins, and
                     100% coverage of the annotated genomic feature by RNAseq
                     alignments, including 3 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:324724"
                     /db_xref="ZFIN:ZDB-GENE-030131-3445"
     CDS             252..5849
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /codon_start=1
                     /product="endoribonuclease Dicer isoform X1"
                     /protein_id="XP_021322789.1"
                     /db_xref="GeneID:324724"
                     /db_xref="ZFIN:ZDB-GENE-030131-3445"
                     /translation="
MAGLQLVTPASSPMGPFFGLPWQQEAIHDNIYTPRKYQVELLEAALEHNTIVCLNTGSGKTFIAVLLIKELSHQIRGENGKRTVFLVNAASSVAQQASTVRTHSDLQVGDYMSEDMTSWPEEMWNREMIENQVLVMTCHIFLHVLKNGVLPLSKINLLVFDECHLAITGHPYREIMKICEGCPSCPRILGLTASILNGKCDPCDLEEKIQNLEKILQSNAETATDLVVLDRYASQPREEVLDCGQYQDQSGLSERLLNELDEALNFLNDCNLSVHREDRDPTFISKQVLNDCRAVLTVLGPWCADKAAGIMVRELQKYIKHEQEELNRKFLLFTDTILRKIHALCEEHFSPASLDLKFVTPKVIRLLEILHEYKPFERQQFESVEWYNNRNQDNYVSWSDSEDDDEDEEAEAKEKTEANFPSPFTNILCGIIFVERRYTAVVLNRLIKEAGKQDPELAYISSNFITGHSIGKNQPRNKQMEVEFRKQEEVLRKFRAHETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPVSNYIMLADSERTKTFQEDLKTYKAIEKILRNKCSKSAECNDFELEPVTDDDNVLPPYVLRSEDGGPRVTMNTAIGHVNRYCARLPSDPFTHLAPKCKTVEMNTGGYRSTLFLPINSPLRVPVTGPVMNCARLAEKAVALLCCEKLHKIGELDDHLMPVGKETVKYEEELDLHDEEETSVPGRPGSTKRRQCSPKAIPECLRGCYPVPEQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPRIPHFPVYTRSGEVTISIELQKSGFSLSAEQLELITRLHQYIFSHILRLEKPALEFKPVEADSAYCVLPLNIVEDSNTLDLDFKFMEDIEKSEARIGIPNTQYTKQNPFIFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLSNVNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRSQTAIDAGVGAQTLPPDFRYPNLDFGWKKSIDSKSFISCPSACMEEDDDHCKLGTSSDSNHTAPESCSMEVSQPPEGAPNTPDEKLETLTLPVTDLNKDCFPNLPNGTQADSDDLPHRSDVCQCSQLGPLERDLSTQTTTSVSVRPSPAGEPQPWPSDECTGRSSDLCDPHVKKPTSKHCPKSETATSTPAPSETSSEDCRSACAGPAWDSPKTLGPNPGLILQALTLSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVNWLPPGYVVNQDKSSTDKWDSDENKDLANGKASDDEDEDDDDEPEEAEVEPSKEDVNVEDDLEYYYEHIRFIDSMLIGSGAFGKKISLQPTDPGYEWKAPKKAHNSHFSPDGGADEFDYSSWDAMCYLDPSKAGEEDDFVVGFWNPSEENCGTDIGKQSISYDLHTEQCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPPEKQSSGGSAELQYGWLKIPPRCMFEHPDAERTLNHLISGFLNFESKINYTFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANVPRSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRALRSLKANQPQVQNN"
     misc_feature    345..926
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="DEXH-box helicase domain of endoribonuclease Dicer;
                     Region: DEXHc_dicer; cd18034"
                     /db_xref="CDD:350792"
     misc_feature    order(345..356,363..365,414..437,549..551,735..737,
                     828..830)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350792"
     misc_feature    order(513..518,585..590,660..662,666..671,678..680,
                     753..761)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="nucleic acid binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:350792"
     misc_feature    1020..1304
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="Partner-binding domain of the endoribonuclease
                     Dicer; Region: Dicer_PBD; cd15903"
                     /db_xref="CDD:277191"
     misc_feature    order(1035..1040,1047..1049,1053..1058,1233..1238,
                     1245..1250,1257..1259,1266..1271,1278..1280)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="Trbp binding interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:277191"
     misc_feature    1323..1901
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="C-terminal helicase domain of the endoribonuclease
                     Dicer; Region: SF2_C_dicer; cd18802"
                     /db_xref="CDD:350189"
     misc_feature    order(1554..1562,1770..1772,1827..1829,1833..1835)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:350189"
     misc_feature    order(1782..1784,1788..1790,1863..1865,1869..1871)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="ATP binding site [chemical binding]; other site"
                     /db_xref="CDD:350189"
     misc_feature    2097..2363
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="Dicer dimerization domain; Region: Dicer_dimer;
                     pfam03368"
                     /db_xref="CDD:460900"
     misc_feature    2865..3233
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="PAZ domain, dicer_like subfamily. Dicer is an RNAse
                     involved in cleaving dsRNA in the RNA interference
                     pathway. It generates dsRNAs which are approximately 20 bp
                     long (siRNAs), which in turn target hydrolysis of
                     homologous RNAs. PAZ domains are named...; Region:
                     PAZ_dicer_like; cd02843"
                     /db_xref="CDD:239209"
     misc_feature    order(3054..3056,3093..3095,3111..3113,3123..3125,
                     3177..3179,3201..3203,3207..3209)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239209"
     misc_feature    4083..>4358
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="Ribonuclease III family; Region: RIBOc; smart00535"
                     /db_xref="CDD:197778"
     misc_feature    order(4134..4139,4146..4151,4158..4160,4167..4172,
                     4179..4184,4188..4196,4224..4226)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    5124..5618
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="Ribonuclease III C terminal domain. This group
                     consists of eukaryotic, bacterial and archeal ribonuclease
                     III (RNAse III) proteins. RNAse III is a double stranded
                     RNA-specific endonuclease. Prokaryotic RNAse III is
                     important in post-transcriptional...; Region: RIBOc;
                     cd00593"
                     /db_xref="CDD:238333"
     misc_feature    order(5184..5189,5196..5201,5208..5210,5217..5222,
                     5229..5234,5238..5246,5274..5276,5538..5540,5571..5573)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="dimerization interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:238333"
     misc_feature    order(5184..5186,5193..5195,5205..5207,5508..5510,
                     5517..5519)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="active site"
                     /db_xref="CDD:238333"
     misc_feature    order(5193..5195,5508..5510,5517..5519)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="metal binding site [ion binding]; metal-binding
                     site"
                     /db_xref="CDD:238333"
     misc_feature    5631..5819
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="double-stranded RNA binding motif of
                     endoribonuclease Dicer and similar proteins; Region:
                     DSRM_DICER; cd10843"
                     /db_xref="CDD:380680"
     misc_feature    order(5631..5636,5640..5645,5652..5657,5664..5669,
                     5679..5681,5694..5702,5706..5708,5712..5714,5763..5774,
                     5781..5783)
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /note="putative RNA binding site [nucleotide binding];
                     other site"
                     /db_xref="CDD:380680"
     polyA_site      9664
                     /gene="dicer1"
                     /gene_synonym="fc39d11; fc74b05; wu:fc39d11; wu:fc74b05"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      
tgcgttcaacctttgaccgtaacatcgaaggaatactgtctcaggccccctcccccatctgcagctttgagagtaactcaaggggagaaaagaatgagctgattttaagagctcagataatgatgcccagaataagtgcggcctggtcacagagcaaagtggggaacgcacacgcttgagcattagatggccatgatgcaatgagataaacactggatgactggaggtctcctgcttatcagtctctaagcatggctggcctacagctggtgacccctgcctcctcacccatggggcccttctttggtctcccgtggcaacaggaagctatccatgacaacatatacacaccaaggaaatatcaggttgaacttcttgaagcagctcttgaacataatactatagtctgcttaaatactggctcagggaagacctttatcgcagtgctcctaatcaaagaactctcccaccaaattcgtggcgagaatgggaagaggacagttttcctggtgaatgcagcgtcatctgtggctcagcaagcatctactgtaagaacacactctgatctccaagtaggcgactatatgtcagaggacatgacatcatggcccgaggagatgtggaacagagagatgatagagaatcaggtgctggtgatgacgtgccacatcttcctgcatgttttaaagaatggagtcttgccactatcaaagatcaacctgctggtttttgacgaatgccaccttgcaatcactggccatccttatcgggaaataatgaagatttgtgaaggttgccccagctgtcctcgcattttgggtctcactgcttccattttaaatggcaaatgtgacccttgtgatttggaggagaaaattcagaacctggagaagattcttcagagcaatgcagaaactgccactgatcttgtggtgctggataggtatgcgtcgcagccgcgtgaggaggtgctggattgtggacagtaccaagatcagagtgggctctcggagaggcttttaaatgagctggacgaagccctcaattttctaaacgattgcaacttgtctgtacatagagaagatagagaccccacgtttatctccaaacaggtgctgaatgactgtcgtgctgtgttgactgtgctgggcccttggtgtgcggataaagctgcaggaatcatggttcgggagctgcagaaatatattaaacatgaacaggaagagctaaaccgcaagttcctgttgttcaccgacaccatcctgaggaaaatccatgccttatgtgaggagcatttttccccagcttccctcgacctgaagtttgtcactcccaaggtcatcagacttttggagattctccacgagtacaagcctttcgaacggcagcagtttgagagtgtggagtggtacaacaatcgcaatcaggacaattatgtttcttggagtgattctgaagatgatgatgaggacgaagaggcggaggcaaaggagaaaaccgaagcaaattttccctcgccgttcacaaatatcctctgtggaatcatctttgtggaaaggcgatatacagcggttgttttaaacagacttattaaggaggcaggaaagcaagacccagagctggcttacatcagtagcaacttcatcacagggcacagcatcggcaagaaccagcctcgcaacaagcagatggaggtggagttcagaaaacaagaggaagtcttgaggaaattcagagcccatgaaaccaacttgctcattgcaaccagcattgtggaggaaggcgtcgatatcccaaagtgcaatttggtcgttcggtttgacctgccgacagagtaccggtcgtacgtgcaatccaaaggtcgagcccgtgctccagtctccaactacatcatgctagcagacagcgaacggactaaaaccttccaagaagacctcaagacctacaaggccatagagaagatcctccgaaataagtgctcgaagtcggctgaatgcaatgattttgagctggagcctgtgaccgatgacgacaatgttctcccaccgtacgtcctgcgctcagaggacggcgggcctcgtgtcaccatgaacactgccattgggcacgtcaaccgatattgtgcgcgcttgcccagtgatccgttcactcatctcgctccgaagtgtaaaactgtagagatgaacaccggagggtatcgatccacactcttcctacctatcaactcaccactcagagttcctgtcaccgggccagtaatgaattgtgcaagactggctgagaaagctgtcgctcttctctgttgtgaaaaactccacaaaattggtgaactggatgatcatctgatgcctgtgggaaaggaaactgtgaagtatgaggaggagctggacctgcatgatgaagaggagacaagcgtgccaggaagaccaggctccactaaacggagacagtgctccccaaaagccataccagagtgtctgcggggttgttaccctgtgccagagcagccttgctacctttacgttattgggatggtcctcaccacccctctacctgacgaactcaacttccggcggaggaagctgtatccaccagaggacacaacccgatgttttggcattctgacagctaaaccaataccccggatccctcatttccctgtgtacactcgttctggtgaggtgaccatctccattgagctgcagaagtcgggctttagtctaagtgcggagcagctggagctgatcacacgtctgcatcagtacatcttctcccacatcctccgtctggaaaagccagcactagagtttaagcctgtagaggcagattctgcctactgtgttctacctctcaacatcgttgaggattccaatactttggatctggatttcaagttcatggaggatattgaaaagtctgaagcacgcattggcattccaaacactcagtacaccaagcaaaacccattcatcttcaaattggaggactaccaggatgctgtcatcattccaaggtatcgtaattttgaccagccgcatcggttctacgtggctgacgtttacacagacctcaccccgctcagtaaattcccctctccagagtacgagacttttgccgaatactataaaaccaagtacaacctggacctgtcaaatgttaatcagcccctactggatgtggaccacacatcttcaagattgaatcttttaactccccggcaccttaatcaaaaggggaaagcccttcctctcagcagtgcggagaagagaaaggccaagtgggaaagcctacaaaacaaacagattttagttccggagctctgtgccattcaccccatcccagcctctttgtggaggaaagccgtctgccttcccagcattctctatagacttcactgccttctgacggccgaagagctgcggtctcagacagccatcgatgctggcgtaggggctcagaccttgcctcctgatttcaggtatcctaatttggatttcggatggaagaaatccatcgacagcaagtctttcatctcctgccccagtgcatgtatggaagaagacgacgatcactgtaaactcggcacaagctccgattcaaaccacactgcccccgagagctgcagtatggaggtctcccagcctccagaaggcgctcccaacacaccagatgaaaagctagaaaccctcactctccctgtgactgatctaaacaaagactgtttcccaaacctcccaaacggcactcaggccgacagcgacgacctccctcacagaagtgacgtttgccaatgctctcagctgggccctctggagagagacctatcaacacaaaccactacctcagtttcagtgcggccctctccagctggagaaccacagccatggcccagcgatgaatgtacaggcaggagctcggatctctgcgacccacatgtgaagaaacctacctcaaagcattgccctaaatcggagacggcgactagcaccccagcaccttcagaaacgtcatcagaggactgtagatcagcctgcgctggtccagcctgggattcgcccaaaaccctgggcccgaaccccgggctcatcctgcaggccctgactctctccaacgccagtgacggcttcaatctggaacgcctggagatgctgggcgactccttcctgaaacacgccatcaccacatacctgttctgcacttaccctgacgcccacgagggcagactgtcctacatgagaagcaagaaggtcagcaactgtaacctgtatcggctggggaagaagaagggtcttccgagtcgaatggtggtgtccatctttgacccgccggtaaactggcttcctccaggctacgtcgtgaatcaggacaaaagcagcacagacaagtgggactcagatgagaataaagatttagcgaatggaaaagccagcgatgacgaagacgaggatgacgatgatgagccggaagaagcagaggtcgagccatctaaagaagatgtaaatgttgaagacgacctggagtattattacgaacacatccgcttcatcgacagcatgttaatcggctctggcgctttcggcaagaagatctccctccagcccacagaccccggctacgaatggaaagctcctaaaaaagcccacaactcccacttctcgccagacgggggtgctgacgagttcgattacagctcctgggacgccatgtgttacctggaccccagtaaagcaggtgaggaggacgatttcgtggtgggcttctggaatccctctgaggaaaactgcggcacggacatcgggaaacagtccatctcttatgaccttcacacggagcagtgcatcgcagataagagcatagcggactgtgtggaggctctgctgggctgctatctgaccagctgtggtgagcgagcggctcagctgtttctctgctctctgggcctgaaggtgctaccaccggagaagcagagttcgggaggctctgccgagctccagtacggc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//

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]