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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa02LNT0159200.3

GAAAAATGTATACCCACTTCTTCAATATTATGTCCAAACAAAGGGAAAAGAAAAGGACCGGCTTATTCTCAGTCTATCCTGCTGTCAATTCCTTCATCAGATGCATGTTATGTTCTCACTTCCTTCCAATCTTGACCTTGCCCATTGTGATCTACTGATCTGTAAGGCTGTGAGAACCTTTCAAGAGACAGCTATTGCCTGCACAACATACATATGAACTAATTTTTCATTAGTTTCTGAGCCCGTGAAAATTGAGTCCATCTGGTCAGAAAGAGGTGCTCCAAATTGCATCATCCCCTTCCTTCATCTTGAGTGCGCATAAGCTTGCTAACTGGATTGCAAACCACTCCACACTGTACCTCTAATTGTTTTCCACCGACCGCATGGTTGCCTGAAGATGAATTATTGCGAGCTGAATAACATGGAAAATTCTGGTATGCAATCCAAAGGTGTCAAACCTTGGATATGAGATTGATGTCAATGGAGGTGCGAGCAACAGTCGACATAGTAGTTGACCCTAGTTCCGAAGCACGCACAGGATGCAGCAGGACCACGGCGCCCCTCCCCTACCCGGCTGTGCTCTGCTTGCCGCTGACATTCCCACCAGCTTCGGCTTCTTTTTTGGCCTTGGCTCCAGCTGCGGCCACTCTCACGTCGTCCTCCTGTGGATGGACTCCAACCTCGCCCCGTAGATCGTTGCGAGATGTTTCCTTAACAATAGATTATATGTGCTTTCTGCAGGGTTGTGCATCTCTTCACTTAAACCAAAATTTTCCAGAATAGAAGCAACCAATGTGGAGAAATAGTGTACAGCATAGGAGCCAACCCCTACCACAGATCCATAAATTGTGAGGTAAAATAAACTTTTCCTTCCCATTGGTAACAATTTCATCCCCTATAACGAATAATAGGTCACACCAACAATCAATTTGATAGAACACATTTTTCCATAAGCAAAAAAAAAATCCTAGTTAAAATTGAGTCACTGAACGTTCCTTATCAAAAGAAAATGGTATTACTTCTTGGTCTTCCCACACAGTTTAGAGTTGCCTCATGGTGTATTTTACAACAAACTAACAAAATTACAACAAAAACTATCTTCGCTAATTAGAGCAAGAGATTTCTATGTTTAGACTGGAAAATTCTATAAATAAACTCAGAGTGAGGTGTTTAATAACAAAATACAGTAAGTTAACTTAACAATTTCATATACTTAATAATAAGCTTGATGGAAGTTCCCAATAACAAAATGCAGTCAGTTAACTTAACAATGTTGTCTGCTGATAAGTAATCAATTAGACCATCATGTTATGTAGAAGACTGTCAAAAAAACACAGAAAAAAATAATAATAGGACATTGGAACCATAAAAGTTTGAAGATACAAACTTACAAGGGGATTATGAAACAACACAAATATGCGAACCATACGAAAATCCAAGTGTTGCGCTAAAAGGAATATGTAAATAAAAGGACTATACACGAAAAGAAGTTCATACCAAGCACAGAGATTAATCGAAACAAAGTGGGTACGGTCTAGCTATTAAGAGATGTTATTCAGGTAAAAATCATCCATCTGTATACTTCGTAAAACGGGAATACTTATCCTTCAACCAAAAAGGCCGAAACCACCAAATACAAAACAAATTTTGAGACATTACCGAAATGCATTGGTTTTGAAGTGAAAGGAAAGGCATGTTACTGCAGATTTATTCACGGCAAAAGAGTTGCAACTTTCCAATCACCCCTCCACAAACCCACTCCAAAACCCAATTCTATGACTAAACCCCAAGAAAACCTAAAATACCAAGATGCTATCAGACGCATCTTACAGCGAAAACCCCAAACCACCCCAAAGGCCCTAAACCCTATATAGAACGGCGCTACGATCCCCGTGCAAACGCAGCAGCAGTCCCAAATCCGCCCATGGTGCACCAAACTGCGGGCACGATTATACCTTTGATGGACCGCCCCACGATGGTGGAATCGAAGGCCGCGGTGTCATCGCCAGTGGAGATGATGATGGGCGCGGCGAGCGAGGCTAGGAGTAGGAGCGGATTTGGGAAATCCCATGATACACAAGCGTTACAAATAAATAATGATTTACACAGTACAGCAAGCAGTGCAATGGTTTCTACAAATATAACCGGATTTTAATTTCATAGGCAAATGAAAGACAAGCATAAATTCTACAATGTCAGATAATTCAAATTGTATTGTCATGCTCCACTAAGTAATGATTTTAATGGAAGAATGTTGAAAAAAAAGTAATAAGATTTCTGCCAGAAAACATAAGTTTCAGTTCAGTACAAACCACCCATACCAAGAGAATAGCACCAGTTTTGAATGATCCAAGTGATAGCATCTCAATTCCCTTATATCTCAAGATAAGACAAGAGCATACTGAATGCAGAAAGCAATCCCCAAAACATTGTTTGCTAGCCAATGCTTCTTCGCAGAATACCATATGCAAAAGAAAAATCCTGGGATCGATGTAACAACTTGAGACTTGGTAAACTCCACTAAGAGCGAGTGGAAAAAATGCAGCACGCTGAATGATGACATTATCATTCCATTCTTTTGGAAGAAATCATTTCATGGAAGGCAGCAATGTTGCACTGCAAGCTTTTGTGTACATCATTGATTTATTTTCCTAATGATCGTGAATAATGGCACTACTGGAACTCGCCTTCGATTTAGCACAACACTAATGAGGTAAATTAGAACATGGACAACCAGACAACTACCCTACCCCTCATTAAAAATAAAAAGGCCCAAACCTCCTGTCCCACCTGATGCTGGCCTCCTCCTTTGTTCCCCATCACATCGCTCCAGCCGCTGCTGCCATCTCTCCCGCGCAACATGGTCAGAAATCCGGCCACCCTCACGAGATGGCCACTGGGAAGAGCCTTGGGGATGGGGCTTGGACGCCGCCAGCCACCTGCCTCATGACCGCTACGAGCAGCGGAAGCAGCAGGTCGAGGAACTGCCACCAAGGTTGAGCGGCCATTGCTGTCGCCGATTGAACCGGTAATTTTTTCTCTGTTGTGAAAGGGATGAACACCGCGGCAAAGACAAGGGGAAGGAGGATCTGAGACCCTTAGCCTCCCTGTTGTGGCCGATTCGTCCCCTTGTCATCGTTGACAATGGTGGCAAGCTGCTCAAGGAGAGCTCGATTCTGTGTCCGCTAGATCAACCACAAGCAAAAGTCAGTATTGCTTGAGATCACAACACACAATCATCACAGCTGCACACCTTGGCCCTTGGGGCGAGGCGGCCCATGAGAGTGGCGGTGGCATTGCCGGCATTGTTCTCCTCAATGAAACTGATTGTGGAGTTCATTATGAGCAGTGTGATGATGCCCACGAAGTCCTGCCAGCCCGGCAGCTTCCTACTCCATTGGCGAGAGCGATGGCCATGATCGCCGCGGCCTCCATGACCCAGGACAGCGGGTTCGACATGAACCCCAAGAACCTCAAGAACTTGCTTTCCTTCTTCTCCTTGAGCTTGTTGGGGCCGAAGAGGTTGAGGCACTGCTCGGCATTGGCGGAGGTGAGCCAGCCGGAGACGGCGATCGACAGCGACGACAGCAGCGGCAGCGCGAGGCGGAGGCGGCCGGGTAGAGCAGGAGGTGGCACCGCGATGGGGAGGCGGCGGCGGCGTCGGCATCGGCGTCGGCGGGGGTGGAGAGGAGTGTTCGCCTCCTCGCTTTCTCCATGTTCACCTCGAAGCCCACGCTCGGCGGAAAGGCGTCGGAGCGAGGGGAAGGCAGAGGTGAAGGCACTCGGAGACGGCGACACGACGGCGGCGTCGGTGGAGGTGGAAGCGGCGGCGCGAGGGCGAGGCAGATGTGGACGCGGTGGCGCGAGGCGAAGGCGGAAGTGGCGGCGCTCGGCGGCGACGGCGACGACGGTGGCGGAGGAGGGGAGGCGGGCGACAGCGGCTAGGGTTAGGGGTGAGTGGACCGGCGGCGGAGGAGGAGGATGGCTGAGGGAGAGGGAGGAGGGGCGGCGGCGGCGTTCGGCGGCGGTGCGAGGGGGAGGCGGTGGCGGCGCGAGGCAAGGCAGGAGAGGGAGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.704017
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0159200.3 2 12416990 T C
Osa02LNT0159200.3 2 12418745 G A
Osa02LNT0159200.3 2 12418941 T C
Osa02LNT0159200.3 2 12419150 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0159200.3 osa-miR5537 Translation 4.5 12.004 1 22
Osa02LNT0159200.3 osa-miR5540 Cleavage 4.5 17.837 1 21
Osa02LNT0159200.3 osa-miR5795 Translation 4.5 13.883 1 22
Osa02LNT0159200.3 osa-miR5837.2 Cleavage 5.0 10.027 1 21
Osa02LNT0159200.3 osa-miR166h-5p Translation 4.0 8.696 1 21
Osa02LNT0159200.3 osa-miR1871 Cleavage 5.0 12.037 1 24
Osa02LNT0159200.3 osa-miR1871 Cleavage 5.0 12.52 1 24
Osa02LNT0159200.3 osa-miR1877 Cleavage 5.0 17.814 1 24
Osa02LNT0159200.3 osa-miR1846e Cleavage 5.0 8.394 1 20
Osa02LNT0159200.3 osa-miR812o-5p Translation 4.5 20.563 1 21
Osa02LNT0159200.3 osa-miR5157a-3p Cleavage 4.0 12.61 1 24
Osa02LNT0159200.3 osa-miR5157b-3p Cleavage 4.0 12.61 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0159200.3 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
Osa02LNT0159200.3 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0159200.3 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0159200.3 2 tgw2 Morphological trait Seed RM290 RM550
Osa02LNT0159200.3 2 qSS-2 Physiological trait Sterility RM301 RM263
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