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

>Osa11LNT0093900.3

GCAAACATCCTTCGACTCTATTGCACCGGGTTTCATAAATATGTACATGTTTCAAAGCACCATACTGTGAATATTCAAGATCATAAACCAAAACTAGCACCTTAGCTTTCCTCAAGATACCTACGTCCTTTTGTACAATTACTCAAAATAAGTAGAACTCCACGATTGGTTTCTCATTTTTTGCATTTGTAGTAGTATCCTAACCTATGGACGTAACATGGAGCAGCTACCTGACGAACTTCCGATAGGACACACAACATCTTGCACCTGAAGCTTCAAGATACGCAACCTGGTGGTGTCAAGTATCTCGAGGCATTCCTGGAGATCCGCATCGCTCGCTAAAATCACCCAGTCACCCTCATCGTCTTTGTACTTGAGCTGAAATAGGCCAATTGACAGTTTCAGCCTCTTCGCTATTTCCTCGAGCAGCTGCTCGTATTTCATGGATGGTAGCAATTTGAACCTTATGGTGTCATTCTTGTAGCTCGCCTTTACGACGACGGTTTTGTTGCTTTCGTTAGCTGACTGACTCTTGATGCTCTTGAAAGTTTCGCCGCTTGATGTGGAGCAATCTGTCATGCTGGAAGAGGACGGTAGGCTTTGTTTGGAATTCTTATTGCTCTTGTCAGTCTCACTCTCCATTCTGTATTCTTGTGGCGCAGAAAAAGAATCCCTTGATGATGGTTTGTGCTCCAGTCTCTCCGTCCTCGTGCCAGTTTTCGCAACACAAGTCATTTCCCTTGCAACATATAAACCATTTGGCATATCCTCACAGAATGCCCCACTCAATGTTCTGGTAGAATGTGAGTTTCGAAATAATTCTCCATCGTCCATGTCAAAATTAATTTCACCATTTTGCTTATTCTGCAGTTTGTGGAGTACATCTTGGCCTGCATGTTCTCTTTGTGTTCAACATTCATCAATACAGGCTCTATGGAAGGGGAAACAGATGAAACAAGGCATCCAGTGGAAGGATCATATTTCAGCACTCCCTCGACTCCATGTACTGAACTTATGACGTTCTGGATCTTCTTTAGGGATCGGTTTACCTTCTTTATCTTACGAGATGGCCACCTTGATATTCCATGTTGTCTGCATATCCTTTTCAGCGTAGTAGGACAAACACCAATACTCTTTGCAGCATCTTTCAGGCTGCCAGAGAAGTACTGCTGGAGGACACTTAAGCTAACACTCTTCTCTGTTGAGCTGCGTCTTTTCTCTCCGTCGGATGCATTGCTACACTTTATTAACTTGTTAGTACTTTTTGTATCTGATAGTTGTTCATCAATGCCCTCTATCTGATATTCCAAAGGCGTATTTGTTTTTGTTTCATTCGATACATCAATTTCTCGGCCTGAATAAATAAGGTTAACAGGTGAAGGGCATCTTGTTCCTGATCGATTTTCATTTGATGGCTTTCTTGTAACATCTTCCTTCAACTCAGCATCTGAAACAGTTCTCAGACTTTTGCATACTCTCCGCATAGTCGCAGATATGCTGTCAAGTAAGAGCTGTTGTTCTCCACCACCTTTGCACAAGACTGGAAGAAAAAACTCAAGCACATAGTCATCATTTTTGGTGTATGTGCTCTGCAGCCTAATTGCAACAGCAGCATGAAGACCAAATTTACGGGCATGATTGACAAGTGGATAAGCGTGCATATCATAATCCTTCACATCAGATGAGAAGAAGGGATTATTTGATAAATATGCATTTCCAGCGACACCTTGTCCTTTCTCAAGGGGGTGTTCAGCACAGACTTGGACAAAATCACGCATTCTCGTGTCATTGACATAACATGCAGATTCCTCTATGCAAAGCACTTCTTTGTTCCTTTTACCAAAATTTGCACCATATTCTACTGACACAAGCACATCTCTTTTGGAGCAAACTGGAATCCATGCAAGTGCCAAAGGTAGCAAGTGTGCTTGACAAACAGCTTGCAGAACATCGAATATTTCCATCAATGCTAATTTCTGGTCCCTTGAATAGCTCTGAGAATGTCTCCATGCATTGACAGTGCTTAACTGAACAGACTCAATTGGGGATATTTGGGATTGGATGGATTGCCCGGTTTCCAAATTCCAACTAGTTCTGGATGATTGGGGGTGGCTTGTGTTTGTGGGTGATATAAAGGACAAGAAACTCAGCTTGTCTTCCCGACTGACCCTAGGCATTGACTGAAATTGTGTTTGTAAGGTGTCCATCTGATGTTAGTCATTCTTTCTGTGCTGTGTGTTCAAGTCATGTGTGCCCTTTGATGAAAAGAGATATCACTCTGTTAGACCGTCTAACACAATATCATTTTAATTTCCTGCAGAGCATTCGAAACATTGACCATCTCTAAGCAAAAGTTATCCTTCTCTCGTGTCATTACTACTTCTAACACTGCACAGCAAGACCCACCACTTGAGTTGAAAACCGGCATCGCAAGGGATCCACGGACCTCGTGGCGCCTAGCATAATCAACCCTCAAATACTCCGAGCCATGATAGTACATCACATTCGACGTCCACTCTGGCATGCCGGACATGAAAACCCGGCCGGGCAATCCGGGGAACAGACCGGGTCCTTCTTCAGCCGAGAATGTGAACTGCCTGGAGACTTCCCTGTATCCCGTAAGCTTCTGATCGAGCAAGAACGGCTGGTCAGAGGTAGTCAGCACATGCTGCTCCCCATTCCTCACAGGCATCCAGACCTGCACAAGGATCGCTTCGCCACCCGACGCCTCTTTGAGCATCGCAAGCGCCCTGAGCATCCTCTCCGTCAGTGTGACGCCGTCGAACGGCTTCGGGACAGAGCCAATTCCCGCGGCCACCGGCTCACCTGAAGCTAATCCGGCGGCGCAATCACCTCTTCTTGTTGTTGTACCCTCCTTAGTGATGGAAACATCAGAATCATCTTGCCTAGAATTAGAACCCACAGGAGTCGAGACGTGCAGCAATCGTTCTTGTGATGGTGGGAAACAGGTAAGAGCTGAGAAGATGCTGTCGGCTACCGATGAACCCGCGACGAGGTCGGTGTAGCTGTCGAGGCCATCGAGCGCTGATGACAGCATGAGCATGTCCATGTCCGGCACCGGATCCCCATCCGGCGTCCCACCTCCATCCATCTTCTCAATCCTCACAGCTTAATTACACTCTTCCTCAGCACCCAAAATAAATAAAAAAAATCAAAACTTCTTTTGCCCAAACTACGACGAGGCGCTTCAGCTTCGATTGGAGCCCAGATGGAGGTCGGCTCTCTCCTCTGCTCTGCTCTGCTCGCCGGCCGGCCGCTCGCCGCCGGCGGTGAGGAGGAGGAGGAGGAGGAGAAAAGGGAA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.832601
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa11LNT0093900.3 11 8970195 A G
Osa11LNT0093900.3 11 8970309 T C
Osa11LNT0093900.3 11 8971020 C G
Osa11LNT0093900.3 11 8971389 A T
Osa11LNT0093900.3 11 8971576 T C
Osa11LNT0093900.3 11 8971807 G C
Osa11LNT0093900.3 11 8972133 T C
Osa11LNT0093900.3 11 8972378 A C
Osa11LNT0093900.3 11 8972894 A G
Osa11LNT0093900.3 11 8973169 C T
Osa11LNT0093900.3 11 8973465 T G
Osa11LNT0093900.3 11 8974091 A G
Osa11LNT0093900.3 11 8974120 C T
Osa11LNT0093900.3 11 8974280 C T
Osa11LNT0093900.3 11 8974638 A T
Osa11LNT0093900.3 11 8975123 G A
Osa11LNT0093900.3 11 8975187 A G
Osa11LNT0093900.3 11 8975555 T C
Osa11LNT0093900.3 11 8976367 T C
Osa11LNT0093900.3 11 8976424 A G
Osa11LNT0093900.3 11 8976776 T C
Osa11LNT0093900.3 11 8976812 T C
Osa11LNT0093900.3 11 8973946 A G
Osa11LNT0093900.3 11 8974257 C T
Osa11LNT0093900.3 11 8971561 A G
Osa11LNT0093900.3 11 8972532 C T
Osa11LNT0093900.3 11 8972463 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
Osa11LNT0093900.3 osa-miR5528 Cleavage 4.5 13.46 1 21
Osa11LNT0093900.3 osa-miR5791 Translation 5.0 13.715 1 21
Osa11LNT0093900.3 osa-miR6245 Cleavage 5.0 14.31 1 21
Osa11LNT0093900.3 osa-miR1440b Cleavage 4.5 15.477 1 21
Osa11LNT0093900.3 osa-miR166i-5p Cleavage 4.5 16.86 1 21
Osa11LNT0093900.3 osa-miR528-5p Translation 4.0 13.499 1 21
Osa11LNT0093900.3 osa-miR815a Cleavage 4.5 12.446 1 21
Osa11LNT0093900.3 osa-miR815b Cleavage 4.5 12.446 1 21
Osa11LNT0093900.3 osa-miR815c Cleavage 4.5 12.446 1 21
Osa11LNT0093900.3 osa-miR1853-3p Translation 3.5 19.225 1 22
Osa11LNT0093900.3 osa-miR2866 Cleavage 5.0 21.331 1 20
Osa11LNT0093900.3 osa-miR395x Translation 4.0 7.418 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa11LNT0093900.3 11 nan Morphological trait Seed RM332 RM229
Osa11LNT0093900.3 11 elr11-1 Physiological trait Eating quality RM1812 RM209
Osa11LNT0093900.3 11 qDLR11 Resistance or Tolerance Other soil stress tolerance RM2596 RM286
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