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2024-03-29 16:30:04, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_026025509            2009 bp    mRNA    linear   PLN 07-AUG-2018
DEFINITION  PREDICTED: Oryza sativa Japonica Group aspartic proteinase-like
            (LOC4337744), mRNA.
ACCESSION   XM_026025509
VERSION     XM_026025509.1
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_029260.1) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            ##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 2 indels
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-236               AP014961.1         2174907-2175142
            237-590             AP014961.1         2175634-2175987
            591-651             AP014961.1         2176104-2176164
            652-746             AP014961.1         2176274-2176368
            747-859             AP014961.1         2176470-2176582
            860-1133            AP014961.1         2176676-2176949
            1134-1247           AP014961.1         2177321-2177434
            1248-1312           AP014961.1         2177567-2177631
            1313-1454           AP014961.1         2177723-2177864
            1455-1574           AP014961.1         2177945-2178064
            1575-1663           AP014961.1         2178551-2178639
            1664-1745           AP014961.1         2178747-2178828
            1746-1746           "N"                1-1
            1747-1772           AP014961.1         2178829-2178854
            1773-1773           "N"                1-1
            1774-2009           AP014961.1         2178855-2179090
FEATURES             Location/Qualifiers
     source          1..2009
                     /organism="Oryza sativa Japonica Group"
                     /mol_type="mRNA"
                     /cultivar="Nipponbare"
                     /db_xref="taxon:39947"
                     /chromosome="5"
     gene            1..2009
                     /gene="LOC4337744"
                     /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 2 codons;
                     Derived by automated computational analysis using gene
                     prediction method: Gnomon. Supporting evidence includes
                     similarity to: 47 ESTs, 1 Protein, and 99% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     73 samples with support for all annotated introns"
                     /db_xref="GeneID:4337744"
     CDS             258..1805
                     /gene="LOC4337744"
                     /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 2 codons"
                     /codon_start=1
                     /product="LOW QUALITY PROTEIN: aspartic proteinase"
                     /protein_id="XP_025881294.1"
                     /db_xref="GeneID:4337744"
                     /translation="
MAKRHLLLVTTCLWALSCALLLHASSDGFLRVNLNKKRLDKEDLTAAKLAQQGNRLLKTGSSDSDPVPLVDYLNTQYYGVIGLGSPPQNFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYNSKKSSSYKADGETCKITYGSGAISGFFSKDNVLVGDLVVKNQKFIEATRETSVTFIIGKFDGILGLGYPEISVGKAPPIWQSMQEQELLADDVFSFWLNRDPDASSGGELVFGGMDPKHYKGDHTYVPVSRKGYWQFNMGDLLIDGHSTGFCAKGCAAIVDSGTSLLAGPTAIVAQVNHAIGAEGIISTECKEVVSEYGEMILNLLIAQTDPQKVCSQVGLCMFDGKRSVSNGIESVVDKENLGSDAMCSVCEMAVVWIENQLRENKTKELILNYANQLCERLPSPNGESTVSCHQISKMPNLAFTIANKTFILTPEQYIVKLEQGGQTVCISGFMAFDIPPPRGPLWILGDVFMGAYHTVFDFGKDRIGFAKSAXKSVCRSLFXITEISLYIS"
     misc_feature    456..1739
                     /gene="LOC4337744"
                     /note="Phytepsin, a plant homolog of mammalian lysosomal
                     pepsins; Region: phytepsin; cd06098"
                     /db_xref="CDD:133162"
     misc_feature    order(474..476,483..491,495..497,726..731,777..779,
                     795..797,912..914,939..956,966..968)
                     /gene="LOC4337744"
                     /note="propeptide binding site [active]"
                     /db_xref="CDD:133162"
     misc_feature    order(540..551,1101..1112)
                     /gene="LOC4337744"
                     /note="catalytic motif [active]"
                     /db_xref="CDD:133162"
     misc_feature    order(540..542,1101..1103)
                     /gene="LOC4337744"
                     /note="catalytic residue [active]"
                     /db_xref="CDD:133162"
     misc_feature    663..695
                     /gene="LOC4337744"
                     /note="Active site flap [active]"
                     /db_xref="CDD:133162"
     misc_feature    1191..1286
                     /gene="LOC4337744"
                     /note="Saposin-like type B, region 2; Region: SapB_2;
                     pfam03489"
                     /db_xref="CDD:427332"
     misc_feature    1359..1472
                     /gene="LOC4337744"
                     /note="Saposin-like type B, region 1; Region: SapB_1;
                     pfam05184"
                     /db_xref="CDD:428355"
ORIGIN      
gaggttgctgtatttatcgtctttgtcctcatctttctttcttgctttcctctaccttgactttggcttccccactctctcttcttcttgggaggctgggagctaccagcacaacacaccaaggaagctgaggtgagaacgattgattactttgctggctgctcttagctactactacaactgttttgtcttaatcggttgattacatctcatatttcatcggtttagctcgctctgtgcgttgatttcttgatatcatggccaagaggcacctcttgttggtgacaacttgtttgtgggctctgtcatgtgccttgctgcttcatgcttcctctgatgggttcctgagagtcaacctcaacaagaagagattggacaaggaagatctcactgccgccaagttggcgcagcagggcaaccgtcttctgaagaccggcagttcagacagtgatcctgtccctctggtggactacctcaacacccagtactatggggtgattggcctcggctcaccgccgcagaacttcacggtgatatttgacactggaagctccaacctgtgggttccttcagcaaaatgctatttttcgatagcatgctacctccacagcagatacaactcgaaaaagtcgagctcttacaaagcagatggagaaacttgcaaaattacatacggttctggggcaatttctggattcttcagtaaggataatgtgttggttggagaccttgtagtgaaaaaccagaagttcattgaggcaacacgcgaaacaagcgttacctttatcatcggaaagtttgatggaattcttggtcttggctaccctgaaatctctgttgggaaagctcctccgatttggcagagcatgcaggagcaggaactgcttgcagatgatgtcttctcgttttggctgaaccgagacccggatgcatcctctggtggtgagctcgtctttggtggcatggatccgaagcattataagggggatcacacctacgtccctgtttcccgcaaaggctactggcagtttaacatgggggatctccttattgatggccactcaactggcttctgtgcaaaaggctgtgctgctattgtcgactccggaacttccttgcttgctggtccaacagctatagttgctcaggtgaaccatgctattggggctgaaggaatcatcagcacggaatgcaaagaagtggttagcgagtatggagagatgatcctcaacttgctcatagcacagacagatccgcagaaagtatgcagccaggttggtctgtgtatgtttgacggtaaacgctcagtaagcaatgggattgaatctgttgtcgacaaagaaaacttgggttctgatgctatgtgttcagtttgtgagatggctgttgtgtggatagagaaccagctacgcgaaaataaaacgaaggagctgatattgaattatgctaatcagttatgtgagcgtctaccaagccccaatggagaatcaactgtcagctgccatcaaatctcgaagatgcctaatcttgcattcaccattgcaaacaagacatttattcttacaccagagcagtacatcgtgaaactggagcaaggagggcaaaccgtctgcatcagcgggttcatggcgttcgacatacctccaccacgcggtcctctttggattcttggagatgtcttcatgggtgcttatcatacggttttcgacttcggcaaagacaggatcgggttcgctaaatctgcantgaagagtgtatgtagatcactcttcnagatcacggagattagcctgtatatttcataagctgaaaccaaacatgtatggttttatgatatatagtagctagtacacggacaaacctctttggttgcttctttctgaagaaaaaagaagaacagacatggatgtatgatctacctgatgtgtataaattgaatgatgcagtctgagaaataatcctctgatcatattgtggattctgaaatatatccgagtttcttttttcaa
//

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]