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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa12LNT0122900.1

TTCTTCTCATAGTGTTCACGTCATCTCAAAGATTGCCATTTTCTATCGTAGACTGCTTATATTTCTGAGTCATCTCAGCCAGGCACTTTTGCAGAGATGCATTCTCAGATCTTAACTGGAAGACAAAGTTGGTAAGGAAGTGCACACGATGCAACATCAGCAATTGCAAAATACCACTCACGATCATCACCAAGGAGGCCTAGATTTTGATAAGCAACTTGATATTTAAATGGTCCATTTGCGGAGAACTCAATATGGTTTGTTCCAGTAAGTTGATCTCTATTCATAAATAAGGTGGTTAGGGATGTTACTATTGGAAACCCATCACCCGGTGCTGGTGAGCTCATGAAGTTATTCTTGCTTAGGTCCCTGTCATAACGGTGGACAGGCATCTCTGGTATAGATGGGGTAGTTCCAAACGACGACTATAGAGGACAAATCACGAGTCGAAATTGACTCTAACAAAGTGGTTATCCCTTGCTTTCACTAAATCATGCACCATTGGGAAGGCGCCTCATCAAACATGTCACAAAGCTTGTTCTTCTTAATCTGGAGCTCGTACCACTCTGACGTGGACATCTCGGTAGTTATCAATAATCACTCTGGTACTACTGAAGCCTGAACTCACATTGCCTATTGAGACAAAATTTGGTTTGATGTCATACATATCACACCGAAACATGGTTCCCATTCTTCCAAATGCTATAATGACCTCATATGATATTAACAATATGTCATCTTAAGGACAAACCAATGGCGCGCCTCCTTGGCCCCAAGAACCGCCATGATACTATCAGCAGCACATGGCATGTTGTTGATCCAAACCAACACAAATGGACCATCAAGAGATCTTCACTCTGATCCTTGTTGCCTAGGGCAGCAATGAAGAGAAGACTCCCATAATATTTTCTCAGTTTATTATGCGAACCAAAGCACCACTGATGGGACAATGCGTAGCAAGTCCAAGTTCGATTATATCCGCTCCATTAATTTTTCACCAATCAAAGCCAAATATTCACCTGATCTTTCACAACCAGATCACCTACTGTAACACTATCCTCGTTGAAAAACCCATCAACTGAACCAGTGCCATATTGAATGGCAGCTGGTTTTCCATTCTTGCGATAAGTGCTTGGCTGCTCGGACTTGTAGCGAGTGGAAAAAGCACGCGATCTCACTCAGCAGAGGGTGGAGTCAGTCTAGCGCAGAAGGATGACGTTGCACAGTGCTGACGGCGAGTCCGTGGTACACATCTGCATCCATCCAGTACGTGCCCTTCTTGAAGCTCGACTTGGTGTCTTGATGGCAGCGGCAAGAAAGCAACATAGGTGGTCAGATTCCTTAGCATCGACCTGGGACGAACAGACCTTGGGGCCCTTGTAGAAGAGCAGATATGGCGCTCATCGAACTGCCTCACCGTCGGTCATCATCTCCGCCCCGAGCTCCACCCGCTGGAACCTGAACTCCGCCCCCAGGTAACACAGGTTCGACAGCGGCGGCCCCTGTGAGAGTAGGGGAAGCGGGCTCCAACGCTTCTCCCCCATACTGCCGTTGACAGCCCCTTCCCACTCTTTACTGCTGCTGTCACCTCTCCCTCCTCTAGATCGACGGACAACCGGCCTTTAGCCAATGAGGTCGCGGCAACGACACCAGCTCCACCCGAGGCCGCCCCTTCCATGTGGTCGGATTCTTACGCCGGCGGCAGGAGGCGGAGGCGGGGATGGCGGCTGTGCGAGGCGGAGGCGGCGGCGGTGGCGGCGCGAGGAAGAGGCGGGGCGGCGGCGAGGGGCGGAGACGGAGGTGGGAGCGCGACGCAGGGACGGTGGCGAGGGGCCGCGGTGTGAGGCGGAGGCGGGGACGGCGGCGCGAGGGGTGGCCAAGGCGGCGGCGGAAGAGAGGGAGAGGGAGCGGGCAGAGGGAGAGGGTGCGGGCGGCGGCGGATAAGGTCTGGGGGGTTAGATTAGTGGGCGTCATTTTTGAAGAAAAACCCTATTCTTTCCTTATTTTACAGAGCAGTCCCTTTCCGCGATTTTTCCCCTTCAAGTACTGTTTATAAGGACATATATATAATTACAAAAAATAGAAGGACTTTTTCGAAAAACTTCCACCCGCGCACTGTAGCTATCCGACGTGGCACGCGCGAGCGGCCGCCCAGCCCGCCGCTCTTAATAGTTTCTAATGTAACCCTCCCAGGTTCAAGAGCATTCCCCATCCTCGATGGATCCATGCCGAATTCTGACGGCAGGAAACGCTGCTCGCAGAGAAGTATTCACAGTAAATATATGGCAATCTGATATTATCCTTATCCTTTAATGTCTGACATTTTTTAGTTTAAACATTAAGAAAAAACAAACAGAGTAGTTATTTAGGTAAAAAATAATCTTATTGTACTGCTCATTGAAAATGTAATTGAGCCCACTATGGTGCTCTATACTATAAAAGTAGAAATCAATATGATCTATTATCTATTTTGATCGATGGGTTATCTATTCGTACTATTATCCTAATTAACGGTAATAGAAACATGGAGGAACATTATTATAAAAAATCGTAATTTAGTAGTGACTAAACATTTTTTTTCTCTTTTATATATATATATATGGGGGAAAAGGTAAATTAACTTGTGCTACATGGAGTATGGGATCCAAGATTCAAATTGAGTATATACCCAATTTGAATGAGTATGAATTTTTTTTAAATGTTTAGATATGAACATTAACTTCTTTACTAACAAGGAGTTTGAACTTTTTTTTTTGTTAGATTTTGATTCTAGGTATATAACATCCAAACATATAATTTGTTAGGTATGTAATAATGAATTGTGAAACAAAGTTGAGTTTGAGTTGTTATGTTGTTAGGTATTTGTATGAATCAAATTCATATACCTGATATCTACTTACAATTTGTAAATTTTTAAAAATTTGAGAGAATTTGTGTGTTTTATACCTTGGAGCCTGGGCACCATGTCTCCCAGGTGTACGTACTCCCGGTTGCATCCATCGTCCATCTGTAGCAGGCGACGATCGAGGCATCGAGCCAATTATCGGATCCATCCACCGAACCCGTTTTGATTTTTTTTCACGAAAAAATATTCAGTAATCGTTAATTTTTCCAAGACTAATCGGTGAAATTCAGCAAGAAACCGATATATATCCCTGATTCCCAGCAAGAAATGGCAACAACTCGTTCTCCCCACCCAATTTACGGATCTAGCGCGATTTACTGGCGGCTCAGAGGTAGGGATGAAACTGGTTTGGATAGTTTCCGTCCGTCCGGATCATTTTTCGGATTCGGATAGTTTCAGTCGGAATTATCCGGAAATTCTCGGATTCGGAAACGAATTCAGATATTTTTTCTTGGAAACGAAAATGAATACAGTAAGGGTACTATCCGTCGGAATCCGAAAACGGTCGGAAACTATCCGGAATTTTTTCGGATATCCGCAGACATTGAGTAAATTATATAAAAAACACGTATATATATATATAACTTTTTTATACGGAATCAGACGAAGACAAACTTTATATTAACATTGTAGAGCTCGATGATATTTACAACTTTATTATTGACTATTTTATTATTTTAGGTCATTTATGGGTCTAAATATTCATTATAATATACCATATTAATTTTTACAAAATCTCAGATCTACAATTCAACGACATCTAATGGAGATGTGTTCCATACCAAAGTTGTAGAGCTCAACGGGATCTACCACTTTTTAGTTTATAACATTTGTATTTAAAAGCATTTAAAGTATAATACAAAGAATACAAGTTTTAAAGTAAAATAAATAAAATCTCCAATTTATACAATAGTAAGTTATATATCAAGTAAAAGGTCTTGGGAATAGAAAACGATAATCATATTTGCATATGGATCTCTTAGAGGAACAGCCATGAAAATCGATTTTCACATACGGTTGTGAGACCGTCTATAAAATTGACGATATAAATGTTGGAGATGTTGAACTAAAATAATAAGCGATATCTCTTCCTTGATCAAGAAACTCAATTTGAGGGGTTTTTTATATACCGGTAAATATTCGCTACCGTATTCGTTCCGTCTCGTATTCGCTCCGTATCTGTATTCGATAATATTCGATTTTATTTCCGTATCCGAGTTTTCGATTCCGATTCCGATCAAAAAGAATATGAAAACGAATATGATAAAGCTAGTTTCCGATCCGTTTTCATCCTACTCGGAGGCGGCAGCATAATAAATTGGTGATTCGACGATGGCGGCGGCCGGCCGGATGCCTGGAGCCATTAATGATTTGGTGGTATAGGGCGATCCATCGGCAGGGACAACAAATTTATCTCGGTTGTGGGTGCCATCGCCCATCCCACCCTTCTCGGGTCTGGATCACCTGGAGTTGCAGGCAAATCCACCGGGTGGATTTCACCTAATCTGAGCCATTCTTTTACTTCTATGGCTGAGATCATCTTTTCTAATTAACAACCCTTATAATCAGTTTAAATCGCAGTGATGACCGACACCAGTGGCATCGCTACCGTGATAATCATGTTCGTGCACTGTCATGCATACACGTACGCGTCACGGCGGTGTTGCTCCAGTGAACTGCATGTCCAAAAATGCAGTAACTTTGCCGGTCGTCCATTCCAGCCGGCGGCTGAACCACTTGTCAACCAAATAGACACATCGGCACCACACCGCCGAGCGCTTGCTCATGTTCTGCTAGTGATCTCAGCCACCACCATTATTTGCCGCTCCTGTGCTCCACTACCACTGCAAGGTGATCTCAGCTCAACCGTGTCTTCTCCGTTTTGTAATTGGCCCTGAATTCTTGATCGATGTCCTGATGTGTGCTCGAGCTCGACGCGCGGTTCTTGTTAACAATTCGGGATAGTGTAACAAACGAGTAAGGTACTACAGAATAAGAACCACCCTGGCTTAATCATGACCCTAGAAAAAGACAAACGGTCCAGATTAGGTGAAATCCACTCGGTGGAGTTGAGTCCAACTCCAGGGGATCCACCGTTCCCACATCCCACGGCGTCTTCAGATTTGGTTTCTCCGCCGGCTATTCAGGAACCCATGCATGTAACAGTGTTTTTTACCGTTCTTAATTCTTGATTCATTGTGTAATCACCTTTCTTAATCACACCGTCCCATCTTAATTAATTGCCTTTGATGCAGATCGATGATTCTCTTGTATATTTCTTATGATCCCTATGAGTGGTCTGCTGCATTTTTTTTTCATAATTCTGTATATTCTTTAGTCTGTGGAATGATGAAGCTCCCTAACTCCTTGTAGAAGCGACACGTATATAATGGTTGAGCTCTGTTTTTCTATGTATAGATGTTGCCTGTGGTCTGACGGCTGGCCGGTGGCTGTTCATGCCGACCCAAAGAAAGCAATCCGGCGGCATCAGTAAATGGTGAATATTAGGGAAGGGTCTTTGTTTAGAAACTGTAATTAGGATTGTACGTTCTTTTTAATCAGCGTATAATGTTTCAATGTTAGCCTAAATTACTACACATCTTTCATGGAAATTCTGTTTTTACTAATGTCAATGACGACTAGTTCTTCTGTTGGAAATGTACATGTTGCCTTCTCGTATCTTTGAGAACATACTGATACTTGAATCATCATACTTGCATGTAGCAGCTGTTATATGTTACTCCCTCTGTTTCATAATGTAAGTCATTCTAACATTTCCCATATTCATGTTGATGTTAATGAATCTAGACAATATGAATGTGAAAAATGCTAAAATAACTTACATTGTGAAACAGAGAAAGTATGTATATTATGTAAAAGTAAGTATATACTGCTACTAATTGAAAAAGACAGTAGATACTTGTACGAACTAATTAAAATGAGTACATATACTATCTACTAACTTAAAAAATAAGTATGTACTACTAACGAAAAATCAGTATATACTACTAACTAAAAAAGATAAGATAAGTATGTAGTACTAGCTAAAATTCAGTATGTACTACTATCTAAAAAAATATATACTGCTATTGACTGAATATAAGTATATACCACTCCTAATTGAAAAATAAGTATATACTGCTATTGACTGAAAAATAAGTATATACTACTCCTAACTAAAAATAAGTATATACTGCTATTAAATAAAAAAAAGGATATACTACTGCTATACTACTAAGCAAAAAGGTATATTCTAGTACTAACTGAAAATATATACTACTATACTGGATCCTTAAAATAATTACATGTCTCATGGATTGCATGCTACAATGTGCACATGCACCTTGAATTTTAGGGATGTATCGTTCAGTACCTACCTGGTAATCTTAAGTGGTATATACTGAACTAGTAGTATATGCTTTCGTTTATATCTAGATTAGAACCGCGGCTCATTCAAATATTTTTCTATTCTAGATATTCTCATCTCAATATATGATACCTTCTGCATCTTATAGGATGTACTGATACTTTTGGATCATCATATCAAGTCCCCAACAAAAACACAATTATAAAAAAAAAAGTATATACTGCTACTGGATATTAAAAAAAAACGCATATAGTTCAACAACCAAAAAATCTAATACGTAGCACATACTAAGTCATACAAAAAAACACAGTATGTGCCGTATACTGAAAAAGGAAAGGCATATGCTCTTTCAACGTTGGTTCTGGTACATACCGAATATTATGAAGAACAAAAATCGTTCTGCATATCTAACTACTTTGCATGCAACAGGCGGACTAATTTACGAGTTGCATGCATGCATGAATTGTTACATCATCTATTTATTAATCATTTTGTTTTTTCAATCCGGTTAATATTGGATGATCCACTATCAGGTATATATATAAAATACACAAATCCACTCAAAAATTTTAAAAATTTTCAAATTGTGAGTATATATCTAGACATAAAAATTTGATTCATACCTATACTTAGCGACAAAACATCTCAAATTCAACTTTATTTTATATTCAATTATTACATACCTAACTAATTATATATTTGGATGCTACTCCCTCTGTCCCATAATATAAAGGATTTTGATATTTTGGTTGCATTGTTTGACCACTCGTTTTATTCAAAAAAATTTGTGCAAATATAAAAAACGAAAAGTTATGCTTAAAGCACTTTGGATAATAAAGTAAGTCCCAAAAAATAATAATTCCAAAATTTTTTGAATAAGACAAATGGTCAAACAGTGCAAGCAAAACGTCAAAATCCCTTATATTAGGGGACGGAGGGAGTATATAGCTAGAATCAAAATCTAACAAAAAGATGTTCAAATTCAGTTCAAATTTGTTTGAACTAGTTAGTAAATAAGTTAATGTTTATACCTATATATTTTTTAAAAAATTCATACTCAATTGAATTAAGTATATACTCAATTTAAAACTTGGTGCCCGGTCACCATAAAGCTCCAGTTAATGAAAAAATGTTTCAATTCTTGAAAAACAGTGAAACACAGTCAAATCAGTAGATGAAACAAATGATTTTAAGGACTGAAACACTAAAAATTCACAACGCACACATCCACTATTCTGATGCTCCTCCCTTGTGCGCTCCCGACAGTGAAGCGACGATGTCGTCCTTGAGCATGCTAGTCTTCTTGATCGTGAGAAAAGAAGATCAAGGATGGCCGCTACCTAGTTCTCGAGCTCAAGACAAAAAAAATCACATAACACCAGATCAACATCATGTTCTCCAACACTGGCTCAACATCAGCGCCAGACCTCCCCCTTCCACAACTACCTCCTTCACTCGTGCGCCACAGAGATAAATCTAGCCATCCCCAGGTCACAGGCTCCACTGTGACCTCGACCTCATCCCACCGCTGCAACGTCACCTCCGACGCCTGCTTGTGCTCATCGTCTAGTCATGGAAGAGGGGAAGAGGAGAGAGTGGGAGAAGAGAGGGAGACGGAGAGGGGCCTTGCCTCCCAAGCTTGACATTTCCAGCTTCTTTGATGGCCTTGACGAGCTTGAGCTGCAGCAAGATGTTGTGGCTGCGGTGGTGGACGCCGGACATGGCGGAGACGACGACGTCCACCTGCCGGACGGCGGCGACGAGGCCATCGTGGTCGTCGAGCGACGCCTCGAGGAGCCGCGCGCCCTGCGCCTTGAAGGCCAGCAGTATCTGGAGCTTGTCGATGTTGAGGCCGATCTCCGGCCGCAGCAGGACGAAGGTGGGGTGGCCCTCCGCCAAGCTCGCCGCAACGATCCGCCGGCCGATGTAGCCGCTGCCGCCGACGATGAGGACCCGGCTCTTCTCCATGGCCATGGCTCCCAGCTCTGATGAGTGCCACAACTGACCACGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.132343
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0122900.1 osa-miR5527 Translation 3.5 13.405 1 21
Osa12LNT0122900.1 osa-miR5532 Translation 5.0 8.107 1 22
Osa12LNT0122900.1 osa-miR5534b Translation 4.5 12.697 1 21
Osa12LNT0122900.1 osa-miR5541 Cleavage 5.0 13.217 1 21
Osa12LNT0122900.1 osa-miR5541 Cleavage 5.0 12.29 1 21
Osa12LNT0122900.1 osa-miR5542 Cleavage 4.5 16.817 1 21
Osa12LNT0122900.1 osa-miR5817 Cleavage 4.5 12.102 1 24
Osa12LNT0122900.1 osa-miR5817 Translation 5.0 16.795 1 24
Osa12LNT0122900.1 osa-miR5820 Cleavage 5.0 22.761 1 21
Osa12LNT0122900.1 osa-miR2873c Cleavage 2.5 5.528 1 21
Osa12LNT0122900.1 osa-miR5079b Cleavage 5.0 15.981 1 22
Osa12LNT0122900.1 osa-miR160d-3p Translation 5.0 23.233 1 21
Osa12LNT0122900.1 osa-miR440 Translation 5.0 18.94 1 24
Osa12LNT0122900.1 osa-miR529a Cleavage 5.0 14.375 1 20
Osa12LNT0122900.1 osa-miR818a Cleavage 1.5 14.993 1 22
Osa12LNT0122900.1 osa-miR818b Cleavage 1.5 14.993 1 22
Osa12LNT0122900.1 osa-miR818c Cleavage 1.5 14.993 1 22
Osa12LNT0122900.1 osa-miR818d Cleavage 1.5 14.993 1 22
Osa12LNT0122900.1 osa-miR818e Cleavage 1.5 14.993 1 22
Osa12LNT0122900.1 osa-miR1436 Cleavage 1.5 15.731 1 21
Osa12LNT0122900.1 osa-miR1436 Cleavage 2.0 14.182 1 21
Osa12LNT0122900.1 osa-miR1441 Translation 5.0 19.371 1 21
Osa12LNT0122900.1 osa-miR1442 Translation 5.0 17.193 1 20
Osa12LNT0122900.1 osa-miR1439 Cleavage 3.5 13.801 1 21
Osa12LNT0122900.1 osa-miR1439 Cleavage 4.5 12.855 1 21
Osa12LNT0122900.1 osa-miR1852 Translation 4.5 15.766 1 21
Osa12LNT0122900.1 osa-miR1856 Translation 5.0 19.896 1 21
Osa12LNT0122900.1 osa-miR1860-5p Cleavage 5.0 22.025 1 21
Osa12LNT0122900.1 osa-miR1870-3p Cleavage 5.0 11.173 1 24
Osa12LNT0122900.1 osa-miR1877 Translation 5.0 6.99 1 24
Osa12LNT0122900.1 osa-miR2097-3p Cleavage 4.0 20.006 1 22
Osa12LNT0122900.1 osa-miR2101-3p Cleavage 4.0 9.349 1 22
Osa12LNT0122900.1 osa-miR2870 Cleavage 5.0 16.388 1 21
Osa12LNT0122900.1 osa-miR2876-5p Translation 4.5 20.285 1 21
Osa12LNT0122900.1 osa-miR2923 Translation 4.5 14.062 1 22
Osa12LNT0122900.1 osa-miR3981-3p Cleavage 5.0 13.336 1 21
Osa12LNT0122900.1 osa-miR5079a Cleavage 5.0 15.981 1 22
Osa12LNT0122900.1 osa-miR5161 Cleavage 4.5 13.922 1 20
Osa12LNT0122900.1 osa-miR5494 Cleavage 4.5 15.324 1 21
Osa12LNT0122900.1 osa-miR5505 Cleavage 4.0 22.835 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0122900.1 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0122900.1 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0122900.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122900.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122900.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0122900.1 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus