2024-09-29 10:24:13, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS XM_015757500 5611 bp mRNA linear PLN 07-AUG-2018 DEFINITION PREDICTED: Oryza sativa Japonica Group endoribonuclease Dicer homolog 3b (LOC4348944), transcript variant X1, mRNA. ACCESSION XM_015757500 VERSION XM_015757500.2 DBLINK BioProject: PRJNA122 KEYWORDS RefSeq. SOURCE Oryza sativa Japonica Group (Japanese rice) ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa. COMMENT MODEL REFSEQ: This record is predicted by automated computational analysis. This record is derived from a genomic sequence (NC_029265.1) annotated using gene prediction method: Gnomon, supported by EST evidence. Also see: Documentation of NCBI's Annotation Process On Aug 7, 2018 this sequence version replaced XM_015757500.1. ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Status :: Full annotation Annotation Name :: Oryza sativa Japonica Group Annotation Release 102 Annotation Version :: 102 Annotation Pipeline :: NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 8.1 Annotation Method :: Best-placed RefSeq; Gnomon Features Annotated :: Gene; mRNA; CDS; ncRNA ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..5611 /organism="Oryza sativa Japonica Group" /mol_type="mRNA" /cultivar="Nipponbare" /db_xref="taxon:39947" /chromosome="10" gene 1..5611 /gene="LOC4348944" /note="Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 7 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns" /db_xref="GeneID:4348944" CDS 29..5308 /gene="LOC4348944" /codon_start=1 /product="endoribonuclease Dicer homolog 3b isoform X1" /protein_id="XP_015612986.2" /db_xref="GeneID:4348944" /translation="
MQTISKKFQTSFSSLEKTKKKEYKCYREIHSSNGHECMILHAKSFSIPGQPKQGEEDLQRPSDMTGPHVGLSPHISATAAAALHRANQLSSASSHRRLTHFAFSHSPPPRRRFIPTSSCASPPPNPPNAAAAAMADDEAAVLPPPPPLPPPCRPHRQLRPRGYQVEVFEAALRGNTIAVLDTGSGKTMVAVMLAREHARRVRAGEAPRRIVVFLAPTVHLVHQQFEVIREYTDLDVMMCSGASRVGEWGADHWKEEVGRNEIVVMTPQILLDALRHAFLTMSAVSLLIFDECHRACGSHPYARIMKEFYFGSQWRPDVFGMTASPVATKGASTLHNCEAHISQLELTLDAKIYIVEDRNELESFSPPTTIVNKYYDAYMVDFDNLKSKLQIFSDEFDSLLVGLQESPSNKFKDTDNILETSRKSLSRYHGKILYSLNDLGPIITSEVVKIHIESVKPLCDSEDCIFSKASLCLHMSYFKEALSLIEEILPQGYGELMKSESGSEELTKRGYISSKVNTLINIFKSFGSSNEVLCLIFVDRIITAKAVERFMRGIVNFSCFSISYLTGGSTSKDALSPAVQRFTLDLFRAGKVNLLFTTDVTEEGVDVPNCSCVIRFDLPRTVCSYVQSRGRARRNNSEFILMIERGNLQQQEHIFRMIQTGYYVKNCALYRHPNALSYDLSIQGMYTYQVQSTGATITADCCVNLIRKYCEKLPKDRYFMPKPSFEVTIEDGLFKCTLTLPRNAAFQSIVGPLSSSSNLSKQLVSLEACKKLHQLGELNDHLVPLTEEPMDTDFTTADEKCISGPGTTKRKELHGTTCVLALSGTWIHDSENITLNTYRIDFLCDQEGENYAGFVLLMEPELDDDVAPSKMDLFLIPNKMVYTTVTPRGKVQLNKKQLGKGKLFQEFFFNGIFGRLFHGSRKSGAQRDFIFKKGHEIQWNTESMYLLLPLRDSSYIQDDLSIHWEAIESCAGAVEQLWSSYQGDENVIPVNCIPQKRRGGQEEIIHLANKSLHCSSIKDSVVLSLHTGRIYTVLDLILDTTAEDSFDEMCKGKASPFTSFVDYYHQKYGIIIQHPEQPLLLLKQSHNAHNLLFSKLKYLDGSTGKPLLMEKEQIHARVPPELLIHLDVTTDILKSFYLLPSVIHRLQSLMLASQLRREIGYNQHIPVTLILEAITTLRCCETFSLERLELLGDSVLKYVVGCDLFLRYPMKHEGQLSDMRSKAVCNATLHKHGIWRSLQGYVRDNAFDPRRWVAPGQISLRPFPCNCGIETAFVPSHRRYIRDDPSFFVGKPCDRGHRWMCSKTISDCVEALVGAYYVGGGIAAALWVMRWFGIDIKCDMKLLQEVKFNASHLCSLSKINDIEELEAKLKYNFSVKGLLLEAITHPSLQELGVDYCYQRLEFLGDSVLDLLLTRHLYATHTDVDPGELTDLRSALVSNENFAQAVVRNNIHSHLQHGSGILLEQITEYVRSNLECQGKESEFLQHTTCKVPKVLGDIMESIAGAVFIDTDFNVDMVWEIFEPLLSPLITPDKLALPPYRELLELCSHIGCFLNSKCTSKGEEVIIEMSLQLRDELLVAQGHDRNKKRAKAKAASRILADLKQQQGLSIKQCLSKAKQLDIVTSDLQFDLTSSGTQLSYSDLNDYHILEGLSSVKKEVVLPLKMEKGGPRSALFKLCKILQWPMPEFEFVEQRFRTPIVMDGATTTNFNSFVSTITLHIPDATTITFQGERRTDKKSAQDSASLMMLHKLQELKICICKT"
misc_feature 503..1099 /gene="LOC4348944" /note="DEXH-box helicase domain of endoribonuclease Dicer; Region: DEXHc_dicer; cd18034" /db_xref="CDD:350792" misc_feature order(503..511,518..520,569..592,710..712,899..901, 995..997) /gene="LOC4348944" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350792" misc_feature order(674..679,746..751,824..826,830..835,842..844, 917..925) /gene="LOC4348944" /note="nucleic acid binding site [nucleotide binding]; other site" /db_xref="CDD:350792" misc_feature 1559..1957 /gene="LOC4348944" /note="Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a...; Region: P-loop containing Nucleoside Triphosphate Hydrolases; cl38936" /db_xref="CDD:476819" misc_feature 1919..1921 /gene="LOC4348944" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350171" misc_feature 2135..2395 /gene="LOC4348944" /note="Dicer dimerization domain; Region: Dicer_dimer; pfam03368" /db_xref="CDD:460900" misc_feature 2981..3412 /gene="LOC4348944" /note="PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a...; Region: PAZ; cl00301" /db_xref="CDD:469713" misc_feature order(3119..3121,3206..3208,3218..3220,3272..3274, 3374..3376,3380..3382) /gene="LOC4348944" /note="nucleic acid-binding interface [nucleotide binding]; other site" /db_xref="CDD:239210" misc_feature 3530..4039 /gene="LOC4348944" /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(3584..3589,3596..3601,3608..3610,3617..3622, 3629..3634,3638..3646,3674..3676,3977..3979,4004..4006) /gene="LOC4348944" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(3584..3586,3593..3595,3605..3607,3947..3949, 3956..3958) /gene="LOC4348944" /note="active site" /db_xref="CDD:238333" misc_feature order(3593..3595,3947..3949,3956..3958) /gene="LOC4348944" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 4160..4621 /gene="LOC4348944" /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(4220..4225,4232..4237,4244..4246,4253..4258, 4265..4270,4274..4282,4310..4312,4544..4546,4577..4579) /gene="LOC4348944" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(4220..4222,4229..4231,4241..4243,4514..4516, 4523..4525) /gene="LOC4348944" /note="active site" /db_xref="CDD:238333" misc_feature order(4229..4231,4514..4516,4523..4525) /gene="LOC4348944" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 5051..5281 /gene="LOC4348944" /note="double-stranded RNA binding motif (DSRM) superfamily; Region: DSRM_SF; cl00054" /db_xref="CDD:444671" ORIGIN
gttatttttgtcagttcatcgtagtgaaatgcaaacaatctctaaaaaatttcaaacaagtttttcttctctagaaaagacaaaaaaaaaagaatataaatgctatagagagattcattcatcaaatgggcatgaatgcatgatattgcatgcgaaaagtttcagtataccaggccagccaaagcagggagaagaagatctgcaacggccctctgacatgacgggcccacatgtcggcctctcgcctcacatctctgcaacggccgccgctgccctccaccgcgccaaccaactctcctccgcctcctctcaccgccgcctcacgcacttcgccttctcccactcacctccgccacgccgccgatttatacccacctcgtcatgcgcctccccaccaccgaaccctcccaacgccgccgccgccgccatggccgacgacgaggctgccgtcctcccgcccccgcctccgctgccgccgccttgccgcccccacaggcagctccgcccgagggggtaccaggtggaggtgttcgaggcggcgctgcgggggaacaccatcgcggtgctcgacacggggtccgggaagaccatggtcgccgtcatgctcgcgcgcgagcacgcacgccgggtgcgcgccggggaggcgccgcggcggatcgtggtgttcctcgcgcccaccgtgcacctcgtccatcagcaattcgaggtgattcgtgagtacactgacctcgacgtgatgatgtgctctggagcatcgcgggttggcgaatggggcgccgatcattggaaggaggaagttgggagaaatgagatcgttgttatgacgccacagatactgttggatgctctgcggcatgcttttctgacaatgagtgcagtgagcttgctaatatttgatgaatgtcatcgtgcttgtggaagccatccatatgcacgaataatgaaggaattttattttgggtctcagtggaggccagatgtatttggaatgacagcctcccccgttgctactaaaggtgcttccacactacacaattgtgaagcacacatttctcaactagaactaaccttggatgccaagatatacatcgtagaagatcgaaatgagcttgagagcttttcccctcctacaacaattgtgaacaaatactatgatgcttacatggttgattttgataatctgaaatcaaagcttcagatattttctgatgagtttgattctttgttggttggtcttcaagaatcgccatctaataaatttaaagacaccgataatatcctagagacttcaagaaagagcttgtccagataccatgggaaaatattgtacagcctaaacgatcttggtccaattatcacctctgaggtagtcaaaatacatattgaaagcgttaagccattatgtgattctgaagactgcattttttctaaagctagcttgtgcttacatatgtcttattttaaagaagctttaagtctaatagaggaaattcttccacaaggatatggtgaactaatgaaatcagaatctggttctgaggaattaactaaaaggggatacatttcttcaaaagtgaatacgctaatcaacatcttcaaatcgtttgggtcatcaaatgaagtgctttgcctaattttcgtagacagaattataacagctaaagccgtcgaaaggtttatgagaggaattgttaacttctcttgtttttcaatttcttacttgactggagggagtacatcaaaagatgctctgagtccagcagttcagagatttactttggatttgttccgagctggaaaggtgaacttgctttttacaacagatgtgactgaagagggcgtcgatgtacctaactgttcttgtgtgatacgcttcgacctacccagaactgtttgtagctatgtccaatctcgtggtcgtgctagaaggaacaactcggaatttattcttatgattgagaggggaaacttgcagcagcaagaacacatatttcgtatgatacagactggttactatgttaaaaactgtgcactctatagacaccccaatgctttatcctatgacttgtctatccaagggatgtacacctaccaagttcagtcaactggagcaactataaccgcagattgctgtgtcaacctaattcgtaaatactgtgagaagcttcctaaagataggtatttcatgccaaagccttcctttgaggtgaccattgaagatggattattcaaatgcacattgacgctacctcgaaatgcagcatttcaaagtatagttggccctttaagcagttcaagtaatttatccaagcagcttgtatccctagaggcctgcaagaaattgcatcaactgggagaacttaatgatcatcttgtacctttgactgaagaacctatggatacagatttcactacagcagatgaaaaatgcatatctggaccaggaacaactaaaaggaaggagcttcatggtactacatgtgttcttgctttatcaggaacttggattcatgacagtgaaaatattacactgaatacttacagaattgattttctttgtgaccaagagggtgaaaactatgctgggtttgttctcttaatggaaccagaacttgatgatgatgtggcaccctcaaaaatggatctgttcctgatccctaataaaatggtctacaccactgtaactcctcgcggaaaagttcaactaaacaaaaagcagttaggtaaagggaaattgttccaagaattctttttcaatggaatctttggtagattatttcatggttctcgaaaaagtggagcacaaagggattttattttcaaaaagggtcatgaaatacagtggaacacggaaagcatgtacttgcttttacctttgagggattcttcatatatccaggatgacctaagcatacactgggaagcaattgaatcttgtgctggtgcagttgagcagttgtggagttcgtatcaaggagatgaaaatgtcattcctgtaaattgtattccacaaaaaagaagagggggccaagaagaaattattcatctggccaataagtctcttcattgttccagcatcaaagattcagtcgtgctatcactgcatacaggaaggatatacactgttcttgatttgatcttagacacaactgcagaggactcgtttgatgagatgtgtaaggggaaagcctcaccttttacttcatttgtggactattaccatcaaaagtatggtattattattcaacatccagaacaaccactattgctgttaaagcaaagccacaatgcacacaatcttctcttttcaaaattgaagtatctagatggctccactggcaaacctctgctcatggaaaaagaacaaattcatgctcgggttccacctgaactacttatccatctcgatgtaacaactgatattctgaagtcattttatttactcccttctgtaatacatcggcttcagtcacttatgctagccagccagcttcgcagagaaattggttacaatcaacacataccagtcactttgattttggaagctataacaactttaagatgctgtgagacattttctctggagcgtttagagctgttaggagactccgtgctaaagtatgtggtaggatgtgaccttttcctaaggtatcctatgaaacatgaaggtcagctctctgatatgagatccaaggctgtctgcaatgctacacttcataaacatggaatatggcggtcgttgcagggttatgtacgtgataatgcttttgacccacggcgttgggttgctcctggacagatatcgttgcgcccttttccttgtaactgtggaatcgagactgcatttgttccttctcatagaaggtatatccgagatgacccatctttttttgtgggaaaaccatgtgacagaggtcataggtggatgtgctcaaaaacaatatctgattgtgttgaagcactggttggagcatattatgttggtggtggcattgctgctgcactttgggttatgaggtggtttggaatcgatatcaaatgtgatatgaagctattgcaggaagtgaagttcaatgcatctcatttatgctccttatcaaaaataaatgacattgaggaactggaagcaaaactgaagtacaacttctcagtcaagggccttcttttggaagccataactcatccatctctgcaggaattaggtgttgattactgttaccagcgtcttgaatttcttggtgattctgtgctggatctacttcttacacgtcatctctatgctactcatactgatgttgatcctggagaattaacggatttacgctccgctttggttagtaatgagaattttgcacaagcagttgtaagaaacaacattcacagtcatctacaacatggatccggaatacttttggagcaaattactgaatatgtcaggtcaaatttggagtgtcaagggaaagagagtgaattccttcaacatactacatgtaaagtacctaaggttcttggtgacattatggaaagcatcgctggtgcagtatttatagacaccgattttaatgttgacatggtttgggagattttcgagccattgctttctccactgattacacctgataagcttgcattgccaccttaccgtgagttgctggagctatgcagtcacattggttgcttcttaaattcaaaatgcaccagtaaaggagaagaagtaattatagagatgtcactgcaactacgagatgagctgctggtagcacaagggcatgacagaaacaaaaagagggcaaaggcaaaagcagcatctcgtattttggcagatcttaagcagcaacagggtctttcaattaaacaatgtttgtccaaggctaaacagctggatatcgtgacttcagatcttcagtttgacttgacaagttcaggaacacaactcagttattctgatttgaatgactatcatatcctagaaggtctttcctcagtaaagaaagaagttgtgcttccactcaaaatggagaaaggtggacctcgaagtgcgcttttcaagctatgcaagattttgcagtggccaatgccagaattcgaatttgtggaacaaaggttcaggactcctattgttatggatggggcgacaacaacaaacttcaatagctttgtttcgacaatcaccttgcacatacctgacgcaacaaccattacatttcaaggtgagcgacgtactgacaaaaagagtgctcaggattcagcatccttgatgatgcttcacaagcttcaagaactcaagatctgtatatgcaagacttagcaaagcatcattgagacatgggccaatatgccagttaacgattgcgactagctaatgcgagctacttccctcccaaagtgagatgcgacgaaaatatttctgaaaagctcgatgctccagactgtcactgatcctatgttattttggggaagaagatccctatggtatactaccttgcattacctggatacattgttgtcgagtttccaatattccacgatgtatcgccccaagattcagggacatacctggctacttttctcttatccaacttcaaggtttccgaggtgctctctctatata
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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.
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