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

>Osa02LNT0150000.2

ACCAATCAACTTTCATTTATTGATCCATTTCCACTAAGAATGACAAATACATGTTGCCTGCAATTCGAGTATATAAATTTAAAGCGGAAAAAAAGAACAACTTGATGGACGACTTTAAAGTCTCTTTTCTGAAGAAAATACTATACAAAAGACAAGTAATACAAAGGACAAAATGCTACATGCCAAAATTTTTGTCATTCGTGAGCAAACCATTTCTTTGTAAAACCTCAGCAGACCTGGAAGTCAGAAAGACTTGTTCTAACTTCCAATATTCAGTTGCCTCTGAAGTCTGAACCCCCATCGAATTGAAATGTATGTTAGAAAAAGAATGTCAAATGAGCCTCAAAAGACCATCTCCAGGCACCTGGGTCGATGTTAAATGATGCTTCAAACAGAATTCTGAAGGCGCAGGTTCCAACTGCCAGTCATTTACAGCAGTGCCAAGCTGGTACCTTTTTCTTATCTTATATTCTCATGTAACCACTATCAATAAGCTATACCTTATGAAATTGGAATGGAAAAATTGTACAACCGCTGAACAAATGATATATATACTATGTTGATATTATAGGGCCTATCGATGACTGGAATATATCATACAGTGCAAGCTGAACTTCTCCAGAGCTATGCTCACAGCGAATGAGGTTAGTTAATAAGGGGAAAAACAGGGGCAGGTTTCTCCTAAAGCAGTCCCTCTCTAGGCCACCCAATAACTGCATCACATGAAGGACCAATGAAGTTCTAGCAGACAGTTCCTCCTTCTTAGCAGTGCCCAAAGGCAGTTTCCAGCGTAATGCTGGATCTCTACCAGATGAATCGTTAGATCGTTCACGCCCTGCACATTTGAGATACTTCCGTAGTATTTTCTCAGAAACAAGCATAATATGTGACTCAATTTTCATATCTTCTGAGATTGATGGGTGGTCATGAACCAAAGCTTGCAGAAGTTTGAGATAGCTCTGGTAAGACTCATTCTCGAAATGAATGACTGCTGGCTCAGACACCTCCAAAAGGGAACATGCTTTATGGAATTTCATGAGCAAGGTAGATTCGGAGCTCACTTCACTTGCATGTGACGCAATGGCTGATAGTGTCTCTAAAATTATTCCCATATGCTCAGCATAAAAAGACCACCTGTGTGTCTCATACAATTTAACTATGCCCTGAACAACTAAGAGCTGCTGCGCCATATGATTCTTCAATTTAATAATAGCGTATGATGTTGTTTCCATATTAGCTTCCTCTTCATCATCATTGTATATGTCATTATCTGAATATCGTTCAACTTCAGGATAAGATTCATTTCTATCTGGAATTTCTATATCTTGCATCATCCTAACTATCTTGTCAAACACGACAAATGTTTGCATTGCTGAGTCTTTAAAACATAACAAGATCTCTTTCCATTCCTCCTTGGAGAGTCTGCTTTCAAGTCCTTCTGTTAAACGCTGAAAAACAGATAAACCTGTGCTAGCAGACTGTTTATAAGGACTTCTGATAAAGTTTGTGACAACAGAAGTAACTCTAGAAAGTTCTGTCCGCATCTCATCAAAAAAGGTAATGTACAAATCCACTAAACACTTGACTGCTACTGTTTTAGTTTCAGAATTCCAAGAGTCATCCTCAGTTAGATTAATGTGCCCATTTGGTGTAGAGCTACCAGTGCTAAATAGAGGATAAACAACAGATTCAAAGATATTTCTCCAAAAGGACTGCGAGAAGAGGTGCCCATGATCCTTCAAAATGTCAAAGAGTACCTCTACTGCACCTTTTCTGATTGTTGGTCTTGTGTCAGTTGTCAACCTAGCTAGACCGGCAAGCAGAGGAACCCAGAAATAAACATGATCGTCCTTGTGCAGAGTGGCATTCCCATCAGAAACATCTAAGTTATTTGACTGGTGATCTGTATCCTTTTCATGACAAACAAATCCTTCCTCGGCAAGTTTAACAGCACAGAACCGAAGAAATGCAATAGCATTGAGACTGGCATCACTGCTAAATTTACTGCTCGTGAATGTAATAAGACATTTAACACAATCAGTAAATGTTGTGGTTTCAGTCTCAGTTATGTATGGAAAATAGTCCCGAACAATCTTTTCCATGGTTTCAAATGCCAACAGCACAATACTTTTTCGATCATCAGCAGCAGCAGCAGTAAAAACCGTAAAAACACTTTTCCATCCGGATTTTATATTGTTAACACGACTCAAAACCATTTGGGAGATGCAACGAACGACAAGTTCCCGTACTTCCGAAGCATTGCTCTTCTGCATAACAACTGCAAAAGGTCGCAGGAATTCATTCTGAAAATTGTAATTTGCCAGTTCCTCTCTTTCCAGAAACTTCATCGCTAGTTGCCTCAAAGAGTCCATAACAAATATTGCAACTGAGAGATTTTCTGACGATCCCACAGACACAAAGAAGTCTGATAAAACTTTCCAAATATGAGACCACACCAGACGTATGCGGTTCATATTGTAATGCGCAATCTCCACAATCTTTGTTAGGCAGAAGATGCGAGGTTCTGTAGGTGAGTGCAACTCTGTCATCGAAACTTTACAAAGAGCTTTCACAAAAGCAACAATGGCATCACTATTTAATCTCTGGCTATGAGCAAATATATGATTTAATTCAAAAATGCCAATCTGGTCTAACAAATTTATGTTTGATATGAAGCTATTTATCTGTTCAGGAGTAACCAATGGTGAGGCATTATTTTTAGCTGTTGTGCTGTCGTAAGAACCCCCTCTGACGGCAGCCATTACAGCTGGATTCTGAAGAGCATTAGTTCGCTTCGAAGCTGTAGTGCTACTTGACTTCTGTGTTTTATCTTCTGACTCAACCAGAGGCACTGTCAAAAATGAAGCATCAGTAGGTGCCCCCTCTCCAAGGAGATGTAGATGCTCAAACCGTGAAAGACATGTTAGTACATGCTCCCAGGAATCCTGCAAATAGTCACCATCTTCAATTGCGATGGATATTATAGCCTTCACAGCATCCACATTCTTTTGTTTCATGTCCGCAGCACAATGGAGGTAAGTGAATTTGGCAACAGATGTCACAAAGGCATCTCGCTGTGTCTGCATACACATTACAGCGGTTACATGCACTGCAGATCTGAATCCTTGCAAACACTGTGATGTGGCAGCCTTATCATCACTTTGGTCAAGTGTCACACTGAATGCAGCCATCATAGGGGCCCAACAAACCTCCATCATGAATCTTAAAATGGTAGAATCAGTAATAACATGAAATATAGATTCTGATTTCCCACTCTTTGCTTTGAATTTCTCCTGTATGTTCTTAATGAGTAAGTCGTTTGCTCCAAGTGCCTTGTCTTCAGCCTGTTTCCAGTTGACAAGGTTGATAATGTTATCCAAGCCTAAGAGCTTAATTACACTACTAGGCTGCTTGCTTTGTGGAACTGACGAATCAGCACTCATTTTTATCTCATTTTTGACAATTTGATCATACAATGTACTCAGATAATGTTCAGGCAAATCCTTCCCATCATCAATTCCTCGGTTATTGCGAATGAAATCAGACTTCGACATCTTATCTTTGACCATCGTATTATGAGCATCGGTATTGAGCATAATTACAGAATAAGCAAGAACATATGCAGTATCTGCACTGGTAAAAGAATTTGGATTGCATTTGCAGTATCGTTCAGCAAACTTTTCCATGATTCGATCAATTTTTTGCGCTTCTCCAGGCAACCTGAAACCTCGCAAGTAATACCTAATGGCTTCACCAAAGTCCATACCTTCGAAGTTCAGTGCATCTGCATATGCATGCATTACTTTGATAGGGAATTCATCTCTTTCACCCAAATAGTCCCCGATCATTGTTGCGTTTAAACCAGCAGTATCTCTCAAGAAAGAAGCAACATCTTCTGGGGAATGACCTATTTTCTTGCTTTTAATGAGAAAATCAATACCCTTGGAAGGCTTCCTGTTAAACAAGGAAATTCCTTTCTGAAGTTCTATTTTATAAGTACGACGCTGCTCAAGTGAGGAAGCGTCAGATAGGTCTGGGTTACCAGAGTCTGTTTGCAGTTCATAATCAACAGCACCCCCATCTTCTCCAACAAGGATGTTAGGAATGTCTATCGAATTTAAAGATATTTCAGAAGGTTTGGGTGAAAATTCACCAATTTTCAGCTGTTGGTCCATCCATGAACCCATTGATTTTATTATGGTTGCAAGACACTTGACTGACTCAATCCGAAATGTCTGGTCTTGTGCAGGGGTTAATGTTGTTGCAGATCCAGGAGGAACCCCTAGAGCAGTCTTTAAAAGCCCATTGACAATCCTGCAAAGATCTTTCAAAGATATTTGGTGCATCAACATCACAATCATAGTTCACAAAGACATCAATAATAACCTGGGAGTCTTTACAGATCTTCTCCAAAAGGTTTAGTACAGTCATTTTCTGCAGAAAGCTAGGTTGATGGACATTCTCAAGAACCCTCAGAACAAGCATGGGAAAAAATATTCCAATTTCCTCTTTCAGCCCAGATCTAAATCTTGACAGCAAACCCAAAAATATGGAGCATAACAGTTGGTAAATACTCATTGCTGACAAGGCACTGTTCTTCAACAAGGACAAACAAAGATACTGCTTGATTGCTCCAAGGTACCTGCATTGAAAAAAAAAAGAGAAAAGAACACTTCAGTATAAGAGTTTTATTACCCATTGGAGTCAGAGTAAACAGAATGCTCTTTATGGAATACCCTAAACATAAAAGGTTTTAAATTGTAACCGTATACTTGCAGGAAGCTTGGTGAACAATAATCATATTTTTCAGCATAGCAAATTAGATGGATGAGCATATTTTGAAGGAAAAAAAGAACGGAATAAAGTTCAGTCACTCCTAATGTTATAAATAAAATATCGTGATGCTTGTGCCCTCTCCTGGCCATCATGTTACATCTGGAGCTCATAAATCAACACTTCATGTTTTTATTCCCTTTCCAGTGTATTGTTAGCTCATTAATTATTTTCTTTTTTTAGTTAGTGAAGAGACTTAAACAAATT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.96808
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0150000.2 2 5221420 C A
Osa02LNT0150000.2 2 5221922 C T
Osa02LNT0150000.2 2 5222345 T A
Osa02LNT0150000.2 2 5222614 A G
Osa02LNT0150000.2 2 5222754 A G
Osa02LNT0150000.2 2 5222816 C T
Osa02LNT0150000.2 2 5223193 A G
Osa02LNT0150000.2 2 5225227 A G
Osa02LNT0150000.2 2 5225703 G A
Osa02LNT0150000.2 2 5226294 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0150000.2 osa-miR5533 Cleavage 4.0 20.953 1 21
Osa02LNT0150000.2 osa-miR5789 Cleavage 3.0 11.069 1 21
Osa02LNT0150000.2 osa-miR5803 Cleavage 5.0 17.012 1 24
Osa02LNT0150000.2 osa-miR5179 Cleavage 5.0 20.737 1 21
Osa02LNT0150000.2 osa-miR396a-5p Translation 5.0 16.961 1 21
Osa02LNT0150000.2 osa-miR396b-5p Translation 5.0 16.961 1 21
Osa02LNT0150000.2 osa-miR396c-5p Translation 5.0 16.961 1 21
Osa02LNT0150000.2 osa-miR395w Cleavage 3.0 11.569 1 22
Osa02LNT0150000.2 osa-miR1425-3p Translation 4.5 12.796 1 21
Osa02LNT0150000.2 osa-miR1429-3p Cleavage 4.5 15.585 1 21
Osa02LNT0150000.2 osa-miR1432-5p Translation 5.0 19.997 1 21
Osa02LNT0150000.2 osa-miR444b.1 Cleavage 4.5 21.768 1 21
Osa02LNT0150000.2 osa-miR444c.1 Cleavage 4.5 21.768 1 21
Osa02LNT0150000.2 osa-miR1877 Cleavage 4.5 7.851 1 24
Osa02LNT0150000.2 osa-miR1320-3p Translation 4.5 12.77 1 21
Osa02LNT0150000.2 osa-miR2101-5p Cleavage 4.5 12.779 1 22
Osa02LNT0150000.2 osa-miR5156 Translation 5.0 14.431 1 24
Osa02LNT0150000.2 osa-miR5485 Cleavage 4.0 23.555 1 21
Osa02LNT0150000.2 osa-miR5486 Cleavage 5.0 17.074 1 21
Osa02LNT0150000.2 osa-miR5519 Cleavage 4.5 18.051 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0150000.2 2 qWIJ-2 Morphological trait Seed RM233A RM8
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