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

>Osa11LNT0109900.1

GTTTCTTTACTACAGAATATATATAATTTTCAAGGAATTAATTAATAGTATAGGGCAAAAGAAATTATATTACATGAACAACTCCACTCTACAACCTTCCTTCCTCAATTAGATGAACGCCTACGTGAAAATGGAAATATAATTGAAAGTGTTTAAAATTGATTCTAAACACTGCCGATTTATTTTCCTCCAAACTCTCAAATTCTTTAACTTTTTACATTCAAACATACACCTCATCCTTCTACATATAAACTGAGAAGAGAAATCTTAAGTCTCAAAGATCAGAATGTTTCCTCTCATTGGACTTACTTTTGTATATGCCCGAAGCTTGCCATTTTATATTGGTTTGGATCATAACACTCTCCTATTCATCCCCATCCCGTGGTCCGTTTAATCGTTTACTACATGAGAGAGAGGAGAGCAGCATAATAGCGTGACATACCAGGTGGTTAATTTGATGGCATTTGGAACATGAGGAAACTTAACCGGCCGGTGGAGCGAGGAGGACGAAGCTGATATCGATCTGCGTGCAGTTTCGATTCATCAGTGAGGGACGACGAGAGTAGGAAGATATCTACATGTTTGAGCCATTATGTTCAGGTTCTAGAGCAAGGTTTGTGTATTTTGTATTCATCCCCATTGTGTGTTTCCTTTACTGGGCGAGAGAGCGAACGAAAATAGCATGACACCCGGATTCTAATGCAAACCTCAATGCTAAACTTCAGGTATGGATTATTAAATTGCAGCTCTTGAATTCAGGCATGTAAACTGAAGAGATGTTTCAGTTTCAATCTAGGATCTGCAGCTTTTCCCAGGAGAATCACAAGGCAATGATGGCAATTCGGACTTTCGTATCTTTTTAGAAAGAAACTCTAACAGTTGAGTTGATGCTCTTATGGGTTAAGATCAATACTATACGGAACTAGGCATGGCAAAGAATTCATCTTCAGAAATAAACTTTTTTTTCGAGTGCTCAATCACCACAGCGAAAAACTTGTCAAACAACACATCACAAGATCACACAGCAGAAACCGATCCATATGTTTGTTGTCATGACTCATGACTCCTGAATACATCATACAACAGAGTTTACTCAACTCCAACAATTGTAAATTGTATACATCTGAAGAGAAATATTCCCTTGGTGATCAACTGATCTTTCCCAATACTCATGCTTTTCTGGCCCCTATTCTATCTATGTACAGTACCAAAAATTGATTGAATGAATGATAAAACAATGAGCCAGCAACCTTTGAAGAGGACTGACATGTTTGTCTGCCTAGTATACTTCATCTCCAATAGGATCAACATAAAGGCGAAGATGGTCACAACAAGAGTAAAGCTCCCCTGGATTGCTTACTTCTTGGCGCTCACTTTACCATTGGGAGCTCTCTTTCCATCAGCCGCACTCAAACTCAACTGTTTTCCGTTCTTGGTTGACGCCGATGGAGGTCCGTTTATCTTTTTTTGTAATGGTGCTGCCCTTTTCGCAGGATTCGTGCTTCTGATGTCTGTGCTTTTTGCACCCTTGGGTTGGGCCTTCCTTGCAATTGAGGCACTCCCATTTGCAGAACCTGGAGCTTTTGGTGCACTTGTTGGACGCACCATATCTTGTTCTGACGAGCAACTGGTTGTGACCTCAAAGTCATCAGAATCCTCTGTTGCGACAGACCCAGCCCAACTCCATTGCGGCTCAGGACTGTTTCTTTGATAGAAGACTACATCTTGTGTAGCATCAGGTCCCAATTCTAGTAGGGAATTGCTGCTACCAAATTGGGAGTTGTTAACCCATTCTCCCAAGGCTGCTTCCTTCTGAGAACTAGTATCAAGCCATGAAGATGTATCATTCTCTACATCTGGCAATTCAAAGTTTCGTTTCTTCTGTCTGGGAGTGCCATTGCTTCTGGTCTCTAGATTTCCAACTTCTTCCATTGGGTTCCTGAATGCAGGAGGTGCGCTGCCCATCCTCATTCTATATATATCTGGGCTTGATTGTGTGCTTCGTATGCTTTCAGTTTCACCATCTTTCTTAGCCAATGCTGCCTTGAGGCAAGCTATCTGTTCTTTGAGCTCTTTGACTTCTCCCCCTTCCTTGTTTGACTTAGCTGCTCCAAGCTCAACAGTAGCAACTCGCTCTGCAAACTTCAAAGTGCTTATTGACTCACCAATAGCATCTGGTTCTGGGGCTATGTGAACAAACATTAATGTTTTTGCTTGTCCTCCAAGAGAATCCTGCAATAACTGAGTAAGTTTGCTATTTCTGTAAGGAACATGTGCATTTTTCTGAGCAAGGGATGCGATCACATCGCCTAGTGCTGCTAATGACTTGTTTATGTGTTGTGCCTCCTTCAGCCTATCACCTACAACCTCAGATTTATCAACTCTTTCACTACCAGCTAAATCCACAAGATGCATACAGCCTCTTAGAACTGTCCGGGATGTCAAATCTCTTCCCTGAACATGAACTGTTAGACAGCTATGGGAGCGGCTACTACGGTCATTCATGGCTGTTGAGCATACTGCACGGTTCTTTTGGCCAAGATTCATTAAATCAATCACATCGGATGTTGAAGTGACTGGTACTATGTTTGCATCAGGAACTGCTATACCTTTCTGCGAACTATTTTTAATGTCCACTTTCTTGTTTCCACCATTCTGAAGGAGATCTCTCACTTGTTCATTGTAGATCTCAATCATCTGCACAGAAATTTCATAACAAAATGTATCTTTCCTCTGTGCTTGAATGTTGAATAGGTCATTTAATGCTCTATAGTTGACACCAAGTCCTTCTTCCGTCAATACTTTAGGACCACTCATTGTAAAGGTCTTCCCTGACCCGGTTTGTCCATATGCAAATATACAAACATTGTATCCATCGAGCACAGAACGGATTAAAGGTTGCATGTCCGCAAAGACCTGTTCTTGCGTGGCTAATGGTCCAAAAACCCTATTGAAAGTAAAAGATTTCCGGGCATCTTTTCCATGTTTTGATGGAGTCATGACAGTGATAGTTCTATCTTCAAGTCCAGCGACACTGCTTGAGGAACTTACCTTTCCAGGTAAGAAAGGTCGTACTCGACAATATACTCTAATATTCCCTCTAAGATCTTGTATTTGGTTGTATAGCTTACGGTTTTCCTCAAGAACTTTATGATACCCAGAAGCCGCATGAGAAAGAGTGTGCACATGCTTCCCAAGCTTATCAAGGTCTTCAGAGTACTGCAGTTTGATGTGCTCCATCCCAGACTTCATAGTTGCAAGATTACTTTTCAAGTCCTTGATATGTTTCTGTTGCTGATCAAAATATTTATCTGTTTGCTTTGCCTGTATATGCTCGACCACATTTTCACCATTCACTAGTACAGCAGTGCTGACTTCTTCCTTCATACTCACAGAAGTATGGTCTTCTTCATCCATATTCCCTGTACTGCATGTACAAGTTGACTCCATTTCTGGTGGTGTATCTGCTCTGGATAACAACTTATCATCATTAGGATCCAAAGCATGTTTCACCGATTCATTCTGGTTTGCAGTACGACGCTCAAATTCGTGAATAACTCTGCTCAACAGTGATTCTACAAGCGACGGTATTTCTTCTGGCTTTTTATCTGAGAGCATTGTTTGGACAAGCATTCTGATGGAGTCTGGAGTAGTTCTTTCCACATGCTCTAGTGAAAAATCAAGACCTAAGCTTTGCTCTAGTGATACGCCATCTCTGAGTAACTCTGCTGAGTAGCTTCTCACCATCGTCTTCACAAAAGGCTCAGAGTTCTTGCGGATGAAGTGCTTTCCAGACATTGAAGGCTTTAGAATGCCACCATATTTTAATGGAGCTGATCTTCCTACTTGCTTACTTTCACTGAATGACCTCAGAGAAAGAACACAGTCTACAACTCGAACTCCTTTTCCACCCTTTTCTAGATCGGATGCCTCAAATGTTGGGAGACCCAAATCTTGTAGGCCCATGAGGAAATTCCTCACATTCTCGAAGTACTGATATGCACAGAGAGCTGCACCATCTGCAGAGTCCGAGGGGGCCTCCACAACCTTGGGCACGCTACCAGGTTGAACCTTATTGAGTGCATTGCAAAGAACAATGCCATTCCTCAGGCCAAGCCGGAATTCCTCCTCGGAGGGCTCTTCTGCAAGGTCCTTTCCACACACCACCCCAACTACCCTTCGCAACCAGTTGGCTGCTTCATATCTTCTTATTGCGGCCTCCTCAGCCTTGCGCCATTCCATGTCGATGCTCCTCCCAACCCCAACCACCTCCCCAACCCCACCTCCACCACCATCCCCGTTCCCCCGCAGCCCGTCCTCCACGACGGCCGCCGTGGCCACCACCGCCTCCTCCCCCTCCGGCGACCCCATGAAACCCGGATCACCCCCAAATCCGGCGACCCGACCACCGCTGCTCCGCCCGGAAAGATCCCGCAACACGGGGATGGGAGGATGAGCCGCGGATTGGAGGAGAGATCGGTGGTGGTGGTGGTGGAGGGGGGGGAGCTCTTCTTGGAGCTCTTGCTCCTCCTCCTTCTCCAAATGGCGGGGTTGATAGTTTTTTGAGGCGGGTGGTGACG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.754986
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0109900.1 11 27161629 T C
Osa11LNT0109900.1 11 27157724 C T
Osa11LNT0109900.1 11 27157733 A G
Osa11LNT0109900.1 11 27157843 A G
Osa11LNT0109900.1 11 27157895 A G
Osa11LNT0109900.1 11 27157955 A T
Osa11LNT0109900.1 11 27157975 T G
Osa11LNT0109900.1 11 27158162 G A
Osa11LNT0109900.1 11 27158210 A G
Osa11LNT0109900.1 11 27158227 A G
Osa11LNT0109900.1 11 27158349 A T
Osa11LNT0109900.1 11 27158418 T A
Osa11LNT0109900.1 11 27158546 T G
Osa11LNT0109900.1 11 27159191 C A
Osa11LNT0109900.1 11 27159333 A C
Osa11LNT0109900.1 11 27159793 A G
Osa11LNT0109900.1 11 27160074 C A
Osa11LNT0109900.1 11 27159945 A G
Osa11LNT0109900.1 11 27160229 T C
Osa11LNT0109900.1 11 27160735 A G
Osa11LNT0109900.1 11 27160815 T G
Osa11LNT0109900.1 11 27160835 C T
Osa11LNT0109900.1 11 27161020 G C
Osa11LNT0109900.1 11 27161392 T C
Osa11LNT0109900.1 11 27161458 T G
Osa11LNT0109900.1 11 27161480 G C
Osa11LNT0109900.1 11 27161608 A G
Osa11LNT0109900.1 11 27161674 T C
Osa11LNT0109900.1 11 27162539 G A
Osa11LNT0109900.1 11 27162564 C T
Osa11LNT0109900.1 11 27162572 A T
Osa11LNT0109900.1 11 27162653 A G
Osa11LNT0109900.1 11 27162786 C T
Osa11LNT0109900.1 11 27164179 A G
Osa11LNT0109900.1 11 27164836 A G
Osa11LNT0109900.1 11 27164881 C G
Osa11LNT0109900.1 11 27164883 G A
Osa11LNT0109900.1 11 27164886 C A
Osa11LNT0109900.1 11 27164926 T C
Osa11LNT0109900.1 11 27164950 A G
Osa11LNT0109900.1 11 27164979 T C
Osa11LNT0109900.1 11 27164981 A C
Osa11LNT0109900.1 11 27164987 T C
Osa11LNT0109900.1 11 27165151 T C
Osa11LNT0109900.1 11 27165386 A G
Osa11LNT0109900.1 11 27161852 T C
Osa11LNT0109900.1 11 27163216 T C
Osa11LNT0109900.1 11 27163227 C A
Osa11LNT0109900.1 11 27163397 A G
Osa11LNT0109900.1 11 27163648 T A
Osa11LNT0109900.1 11 27163705 T C
Osa11LNT0109900.1 11 27163868 T A
Osa11LNT0109900.1 11 27164071 A G
Osa11LNT0109900.1 11 27158581 A G
Osa11LNT0109900.1 11 27164659 A 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
Osa11LNT0109900.1 osa-miR5806 Cleavage 3.5 17.134 1 21
Osa11LNT0109900.1 osa-miR5821 Cleavage 5.0 18.806 1 21
Osa11LNT0109900.1 osa-miR5829 Translation 5.0 16.639 1 24
Osa11LNT0109900.1 osa-miR395b Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395d Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395e Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395g Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395h Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395i Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395j Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395k Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395l Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395s Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395t Cleavage 4.0 12.859 1 21
Osa11LNT0109900.1 osa-miR395a Cleavage 4.0 12.859 1 21
Osa11LNT0109900.1 osa-miR395u Cleavage 5.0 12.859 1 21
Osa11LNT0109900.1 osa-miR171f-5p Cleavage 5.0 18.119 1 21
Osa11LNT0109900.1 osa-miR171h Cleavage 3.5 10.71 1 21
Osa11LNT0109900.1 osa-miR416 Translation 5.0 20.328 1 21
Osa11LNT0109900.1 osa-miR437 Cleavage 3.5 7.899 1 21
Osa11LNT0109900.1 osa-miR528-5p Translation 4.5 15.298 1 21
Osa11LNT0109900.1 osa-miR395m Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395n Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395p Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395q Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR395r Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR1426 Cleavage 4.5 16.487 1 21
Osa11LNT0109900.1 osa-miR1429-5p Translation 4.0 12.515 1 21
Osa11LNT0109900.1 osa-miR1847.1 Cleavage 4.0 11.532 1 21
Osa11LNT0109900.1 osa-miR1857-5p Cleavage 4.5 13.325 1 21
Osa11LNT0109900.1 osa-miR1857-5p Cleavage 4.5 13.695 1 21
Osa11LNT0109900.1 osa-miR2055 Cleavage 5.0 23.74 1 21
Osa11LNT0109900.1 osa-miR2101-3p Translation 4.5 13.358 1 22
Osa11LNT0109900.1 osa-miR395y Cleavage 4.5 12.859 1 21
Osa11LNT0109900.1 osa-miR5150-3p Cleavage 4.0 16.558 1 24
Osa11LNT0109900.1 osa-miR5491 Translation 5.0 22.595 1 21
Osa11LNT0109900.1 osa-miR5519 Cleavage 5.0 14.475 1 21
Osa11LNT0109900.1 osa-miR5523 Translation 4.5 12.51 1 22
Osa11LNT0109900.1 osa-miR396c-3p Cleavage 5.0 10.834 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0109900.1 11 FON3 Morphological trait Panicle/flower RM4601 RM1233
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