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2024-03-29 21:20:31, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_015775890            4728 bp    mRNA    linear   PLN 07-AUG-2018
DEFINITION  PREDICTED: Oryza sativa Japonica Group protein argonaute 13-like
            (LOC4334374), mRNA.
ACCESSION   XM_015775890
VERSION     XM_015775890.2
DBLINK      BioProject: PRJNA122
KEYWORDS    RefSeq; corrected model.
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_029258.1) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Aug 7, 2018 this sequence version replaced XM_015775890.1.
            
            ##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##
            
            ##RefSeq-Attributes-START##
            frameshifts :: corrected 1 indel
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-131               AP014959.1         32813936-32814066
            132-337             AP014959.1         32814466-32814671
            338-473             AP014959.1         32814756-32814891
            474-607             AP014959.1         32815005-32815138
            608-717             AP014959.1         32815229-32815338
            718-824             AP014959.1         32815410-32815516
            825-963             AP014959.1         32815973-32816111
            964-1080            AP014959.1         32816190-32816306
            1081-1188           AP014959.1         32816498-32816605
            1189-1260           AP014959.1         32816694-32816765
            1261-1380           AP014959.1         32817031-32817150
            1381-1546           AP014959.1         32817232-32817397
            1547-1668           AP014959.1         32817481-32817602
            1669-1776           AP014959.1         32817723-32817830
            1777-1778           "NN"               1-2
            1779-1809           AP014959.1         32817831-32817861
            1810-1949           AP014959.1         32818050-32818189
            1950-2012           AP014959.1         32818274-32818336
            2013-2076           AP014959.1         32818416-32818479
            2077-2212           AP014959.1         32818575-32818710
            2213-2286           AP014959.1         32818815-32818888
            2287-2381           AP014959.1         32818984-32819078
            2382-2413           AP014959.1         32819175-32819206
            2414-2544           AP014959.1         32819758-32819888
            2545-2777           AP014959.1         32820009-32820241
            2778-3585           AP014959.1         32820330-32821137
            3586-3744           AP014959.1         32821229-32821387
            3745-4728           AP014959.1         32822526-32823509
FEATURES             Location/Qualifiers
     source          1..4728
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /cultivar="Nipponbare"
                     /db_xref="taxon:39947"
                     /chromosome="3"
     gene            1..4728
                     /gene="LOC4334374"
                     /note="The sequence of the model RefSeq transcript was
                     modified relative to its source genomic sequence to
                     represent the inferred CDS: inserted 2 bases in 1 codon;
                     Derived by automated computational analysis using gene
                     prediction method: Gnomon. Supporting evidence includes
                     similarity to: 1 mRNA, 7 ESTs, 3 Proteins, and 99%
                     coverage of the annotated genomic feature by RNAseq
                     alignments, including 57 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:4334374"
     CDS             586..3738
                     /gene="LOC4334374"
                     /note="The sequence of the model RefSeq protein was
                     modified relative to its source genomic sequence to
                     represent the inferred CDS: inserted 2 bases in 1 codon"
                     /codon_start=1
                     /product="LOW QUALITY PROTEIN: protein argonaute 13-like"
                     /protein_id="XP_015631376.2"
                     /db_xref="GeneID:4334374"
                     /translation="
MGLSLNIDISATSFFKPVTVIQFVEEFLNIRDTSRPLSDRDRVKIKKALRGVRIETNHQEDQIRRYKITGITPIPMSQLIFPVDDNGTRKTVVQYFWDRYNYRLKYASWPCLQSGSDSRPVYLPMEVCKIVEGQRYSKKLNNKQVTNILRATCQRPQQREQRIHEMVLHNKYTDDRFAQEFGIKVCNDLVSVPARVLPPPMLKYHDSGREKTCAPSVGQWNMINKKMINGGTVDNWTCLSFSRMRPEEVQRFCGDLIQMCNATGMSFNPRPVVDVRSSNPNNIENALRDVHSRTSELLAREGKGGLQLLIVILLEVSGSYGKIKRVCENDLGIVSQCCLPRHASRPNKQYLENVALKINVKVGGRNTVLERAFIRNGIPFVSEVPTIIFGADVTHSTXGEDSASSIAAVVASMDWPEITKYRGLVSAQSHRQEIIEDLFSVGKDPVKVVNGGMIREFLIAFRKKTGRRPERIIFYRDGVSEGQFSRVLLHEMDAIRKACASLEEGYLPPVTFVVVQKRHHTRLFPEVHGRRDMTDKSGNILPGTVKDRQICHPTEFYFYLCSHAGIQGTSRPTHYHVLYDENHFTADELQTLTNNLCYIYARCTHAVSVVPPAYYSHLAASHAHCCIKGHSSGSGSTPGNEHDIVKNSAPTLQILVKVLDFQIVPLTMKLKSSAEDIVALALSKHRVSLHDVYVYHGRRVIAKSLTLESLKADRDSTFLIMPRMRGGCNDTIGGFKCIPLEQHIRSLGDSLFEIIWIPPDLRVSGFCSYLIILGKPARKIICQLLKLLEIIHAANRFASRFTIADLVFLPDLGCIAFKKGVKIRWNLRREEYKLNMGDVASIISCWFRFNRRKLEALEAGIHELRPGQGDSPMFVDILVKDLRSPTHETGLSANYRGFYKNCSALRSCSAHMNLFTSLDIRKDFMVGSADWGNFVKALGDIKLPGWYRTAMRSPEMRKVLFFEFNDPHTGELRGKRYRALSVFSWLEFARIFIKHMKKGLCTDKQATALLCVIFSNIVPVVEKKLTYSYRPPAKEKSNESFTVEEILDPS"
     misc_feature    634..978
                     /gene="LOC4334374"
                     /note="PAZ domain, argonaute_like subfamily. Argonaute is
                     part of the RNA-induced silencing complex (RISC), and is
                     an endonuclease that plays a key role in the RNA
                     interference pathway. The PAZ domain has been named after
                     the proteins Piwi,Argonaut, and Zwille; Region:
                     PAZ_argonaute_like; cd02846"
                     /db_xref="CDD:239212"
     misc_feature    order(781..783,826..828,859..861,871..873,925..927,
                     946..948,952..954)
                     /gene="LOC4334374"
                     /note="nucleic acid-binding interface [nucleotide
                     binding]; other site"
                     /db_xref="CDD:239212"
     misc_feature    1114..2460
                     /gene="LOC4334374"
                     /note="PIWI domain, Argonaute-like subfamily. Argonaute is
                     the central component of the RNA-induced silencing complex
                     (RISC) and related complexes. The PIWI domain is the
                     C-terminal portion of Argonaute and consists of two
                     subdomains, one of which provides the...; Region:
                     Piwi_ago-like; cd04657"
                     /db_xref="CDD:240015"
     misc_feature    order(1543..1545,1555..1557,1591..1602,1609..1611,
                     1633..1635,1642..1644,1654..1656,1666..1668)
                     /gene="LOC4334374"
                     /note="5' RNA guide strand anchoring site [active]"
                     /db_xref="CDD:240015"
     misc_feature    order(1759..1761,1765..1767,2014..2016,2434..2436)
                     /gene="LOC4334374"
                     /note="active site"
                     /db_xref="CDD:240015"
ORIGIN      
ccatccttcatgttctaacctagctataatcttcaactctcactatccattcttccctccccattattcctcaacgcttcgccggcgattcccctctagactctagcgttcgccatggatgcccgccccatgtttcaatcaatcctgagtcaaaatcaagagcaacaaatagggaagtactcaatgagctcatcaagttgcatgggaagacatctcttggtggcaaattgcctgcttatgatggaagaaaaagtctctatactgctggttcactcccttttgaatcggaggagtttgtggttaagctaattgatcccgaaaagaaggataaagaaagggcggagagggagtacaagatcacaattcggattgctggcagaacagacttctaccacctccagcagtttttgcttggaagacagagggatatgccccaagaaaccattcaagtcagtcattgatgttgtcctcagttatgtcacagtgtccagatccttcttctctacccagtttggtcaccggggtgacattggtgagggacttgagtgttggagaggttactatcagagcctgcgcccaacacagatgggcctttcgctgaatatagatatatctgcaacatcattttttaagcctgtgacagtgatccaatttgtggaggagttcctgaacatacgtgacacctcaagacctttgtcagaccgggatcgtgtgaagataaagaaagcattacgtggggttcgcattgaaacaaaccaccaagaggaccaaatcagaagatacaaaataacagggattacccccattcctatgagccagctgatatttcctgttgatgataatgggacaaggaagactgttgttcagtacttctgggataggtacaattacagactgaagtatgcttcttggccctgcctacagtctggcagtgattctcgtcctgtatacttgcctatggaggtgtgcaagattgtagaagggcagaggtactccaagaagcttaacaacaaacaggtgaccaacatccttagagcaacctgtcaacgcccccagcagagggaacagagaattcatgagatggttctccacaacaagtatacagatgataggtttgctcaggagttcggcatcaaggtctgcaatgacctagtctctgttccagcccgtgtgctgcctccacccatgttgaagtatcatgattctggaagggagaaaacttgtgcacccagtgttggacagtggaacatgattaacaagaaaatgatcaatggaggaactgtggataactggacatgtctgagtttttcacgaatgcgtccagaggaggtacaaaggttctgtggtgacctgattcagatgtgcaatgccactggaatgtctttcaatccaagaccagttgtggatgtccggtcatcaaatcctaacaatatagagaatgctctgagggatgttcacagcagaacatcagaactgctagccagagagggaaagggaggcctgcagcttttaattgtaattctgcttgaagttagtggttcttatgggaaaattaaaagggtatgtgagaatgaccttggcattgtatctcaatgttgtttgccaaggcatgccagcaggccgaacaagcaatatttggaaaatgttgcactcaaaatcaatgtcaaggtcggagggcgcaacactgttcttgagcgagcctttatccgcaatggcataccatttgtgtcagaagtcccaacaatcatctttggtgctgatgtcacacactccaccnntggagaggactctgcatcatctattgctgcggttgtggcatcaatggattggcctgaaatcaccaaataccgaggtctggtctctgctcaatcacatagacaggagataatagaagatctctttagtgttggtaaagatccagtgaaggttgtaaatggtgggatgatcagggagttccttatcgcattccgcaagaagactggcagaaggcctgagaggataatcttctatagagatggtgtaagtgaaggtcagttcagccgtgtgcttcttcatgaaatggatgccatcagaaaggcttgtgcatctttggaggagggatatctaccacctgtcacatttgtagtagtccagaaaaggcatcacacaaggcttttcccagaggttcatgggaggcgagacatgactgacaagagcggaaacatccttcctggaactgtcaaggaccgccagatttgccatcctacagagttctatttctacctgtgtagccatgctggcatacagggtactagcaggccaactcattaccatgtcctttatgatgagaaccattttacagctgatgaacttcagaccctgaccaacaatctttgctatatctatgcacgatgcacccatgcagtgtctgtggtcccaccggcctattattctcatcttgctgcatcacatgcacactgctgcattaaaggacatagttcaggtagtggctcaacccctggcaatgagcatgacatagttaaaaattctgctccaacactccagatccttgtcaaagtgctggacttccaaatagttccactgacaatgaaactgaagtcttcagctgaagacattgtagctttagctctatcaaaacatcgcgtctctctgcatgatgtctatgtctaccatggtaggcgagttattgccaagagcttgactcttgaatctttaaaagcagacagggattcaacttttcttataatgccacgtatgaggggtggatgcaatgatacgattggcggtttcaagtgcattcctttagaacaacatatcagatcattaggtgattccctttttgaaatcatatggataccaccagatctgcgagtgagcgggttctgttcatatcttatcatacttggaaaaccagcaagaaaaatcatctgccaacttttaaagttgttggagattatccatgctgccaacagatttgcttccaggtttacaatagctgatctggtgttcctccctgatctgggttgtatagcttttaagaaaggagtaaaaataaggtggaacctcaggagagaggagtacaaactcaacatgggtgatgtagctagcataattagctgctggttcaggtttaaccgcaggaagcttgaagcgctggaagcagggatccatgagcttcgtcctggccaaggtgactctccaatgtttgttgatatattagttaaggatcttagaagccccacacatgagactggtctcagtgccaattatagaggtttctacaaaaattgtagtgctctgagatcttgttcggcccacatgaatttgttcacctctttggacattcgtaaggacttcatggttggttctgctgattggggtaattttgtcaaggctttgggtgatatcaaacttccaggctggtatcgtactgctatgcgatcacctgaaatgaggaaagtactcttctttgagtttaatgatccacatactggggagttacgaggcaaaagatatcgtgccttatcagttttttcatggcttgaatttgcgcggatatttattaagcacatgaagaaagggctgtgtaccgataaacaggcaacagcacttctctgtgtgatattctcgaatattgtacctgttgtggagaagaaacttacttacagttacaggccaccagctaaggagaagagcaatgaaagctttacagttgaagaaatcctggacccatcatagtcatagatgtcggaggaaagacagaatgttgctgtaagctacaaatctcagtatggttggaggatgactctgcaaaggttggagtatgtatgacaaagcgcgaagaaaaagctttcaaggaaagggtttctgaagtttttattggtttgaacagatcctggaaatgaattcatatggatggggagctatatcagttgtagaagttctttttttccttaagttttctgtgtttgtcagtttagcctggtagtgatagactgatagatcctgatgatgtagctgtgtgttagtttgaacgattttctgtttttaagctttttgttcgatgccctggaactgtccaggcatgagtgaccttgtagaaactttcacatttcttttaatagaaatggaggggtattgcccttttgataaagaaaaagggatataatatgttgggctggtattcctgttgatttcaattattctttttatagggcaagcaagggttaaatatggtaaaggtcaagtagttgctttgttagctgtcgtgacttgaagcttatgattgattttttttgacgcaaatcgaaatattctgtttgacgcaatgattgatttgaaatgatgtgttttttagcaacaaattccttttcaaacttttgactttggtttttcgtgtattttctctacagatgcagtggaagatgattgaatgtcttcctggaacatgtgcaagaaattgttaatcatctgcacccctcaaggactgagtgttggttaaaagtagttgttccctgcctccctgggagttagggctttagtagagtttagcgttactagttctcaggaggaatgatgtccagtgcctttcgttaagagttgtgtagaaactgaggtggtcgagtaatcttctctgctgagcgttttcgttttttagctggagtacccagcctaaacttggtttccctttaaagctggcaatacaagctgactctgtttccgtttaaa
//

by @meso_cacase at DBCLS
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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]