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

>Osa05LNT0305400.3

CATGTATTTGTTGCCATCCGTAGTCCCGCATTAGAGAACTCAATGGCTTCTGCAACCAACTGTCTGAACGCTTCTATGTTTTTTGCTAGATTACTTTTCTCCATCAGGTGAAGGACAGATGGTTGCACTAAAGGGAACCGCACAAATGGTAGCAAAGTATTGATGGCAGTGAGCCTCCCTCCAAAGAGTTTCTCTGGTCTTGAAGTGCTTAAGAGCTCGTGCACAGAGGTCCAGTTAAAACAGTCACAAGCCTCCATGCACCATGTTAATATGGCATCCAGAACCCTCTCTTCTGATGTTACAGTCATATGCCCATGCTGAAGAATATCCTTAAATGTTGCCTCATCCAACAACACAAAGTCTGTGCAAGCAGTTGTGCAATAATCAAAGTGTTCTGCAAAATTCCTCTTGCACATTTCTTCAAGCAGTTTACAAGATGGAATTGACGAAACTGCTCGTAGAACTGAACATACTGTGTCCTGCAAGAAACTTTCAGGGGTAAGTCTACACTGAACCAGCTAGCAAATTCACCAAATTTGCAGAAGCCATATCCAATTATCCCATAAAAAAACTAGAAATTAGCCCTGGTGGATGAGCTTCTTCCTGTAGGACACGAATCCTTTGAGAGGAATTCCATAATTCTTTTACAGCATTCAAACTGAAGAGCCGTGATCCCAAACTGGTCTGACAATAGGAGCAGCTCAACCAACACTGGTGTGATTTCCTCGATATCCACCTTAAGTTCCCCACTGTACATAAATTGGATGAGGAGAAAGAATGCTTCGACGGGAACATCTTCGAAAAATACATTTGAAGCACTGCTTTCTTTCATTCCATTTGTGAACATCTTGTCAAATGTCATGCTCCACAAGCTAAGGATGAGTTTGTGAGCATGAGTAACAAGACCATGTCCATTTACATAGATATTTACATCACTGTGCTCACCATTTACAAGGAACTGTTCAATTTTCTGTGTATTTAATGGAGCTTTGAAAGGGAAATAATAAAATTGATGAGCTTGAGAACCACCACTTGATAACTGTATTTTTTTGCTAGACTCAGAAACTGCATCACTCATCTTCAAACAGCCAATAATTTCTTCACAATACATTACCAATGGTTTAACTTTAAATTGTGAACTCAACTCCAGCAGTGAAACCAGTTGCCATTCCGAAATCTGCGTAGAACCTGTGTAGATGTACTCAAGAAGGGAGTGCAGAACTGGGTAGGAGACAGATGGAAGCTCAATAGCTGGTCGACTCATCATCAGGTTAAAAGGGAAATCACCACAAGAACCCAAGACAACTTTGTGAGCTGGGACAACCTTTCTTTCGCTGCCAACCACAAATATAGAATCTGAGAAATCCCAGTTCTCTAGAAAGTTTGCAAGTGCCCTTTGGTCTAAGCCATCTTTTGATTCTTGTTTTCTTGTATGCCCTCCAGCACCATCCGGCTCAACATATGCACACTCAATTTGGCTCCAAAGGATGCTGTTTTGAGGAGCTGATGGCATAAGACTTATATTTCTGTATCCAACATGCTTGTCCCAGCTGGATAGTCCCACATACTGAACATTTCGGTTGGGATCAGGGTCAAGCCATTGGAACAGGATGTTGTTATTTGGATGTCTTCCTTGCCCGATGCTTATCAGTCCATCATAGATGCTGATCCAGTAGCTCTGAAAAGACGAGGAGCAACATAGGCCAATGCCAGCAACATCAACAACAGTCTTTCCATCTACTTCAATTTTCAATCTTTTGTTCCTATGGCTGCCCAAGATCACAATGTAGTGACGACTGTTATCCATTTTGTAGTGATAATGCTGGCTCCCAGGTTGTTCGCGGAACACCAGGGTAACATCATTGTGTGCAGATGCCTCAAAGGTGATGCACCCGCGACCAGTCTCCCTGAACCGAAACTCCTCATCCCAAGCACACTCGAAGGGGGCAACTGTTATAGATCTTTTTTTCTCCTCCACTTTCATCGTAAACAGATTTCAGGTTTACCACCAAACTTGGGCAATCAAGCGTCAATGAGTATAAATATCTGTCAGAAAATTGAGATAACAAAAAAATGTATGAGTGGTCAACTAACCAAATAGTTCATGCATAGAAGGACAACATTGACTAATATCATCCAGTTTTTTTACTCTCCTTTTGTTTGCATAGAAAACATGTTTATAGCTAACTGTGGGTCAGTCAACCAAATTCATCGTCCCAAGGAATCTGCACCCAACAACTACTGACAATGAAGAGAAAGCCAATTCTCGCATCACATTCCTTTATATATTCGACACCAATGAGAATAGTAGTGAAATTAAAATACTGTACAACACAACCCAGCAGATACCGCTACCCATATTCATCAGCAATCTAATTAGGCTATTCCCAACCCAAGACATTAGACATAGTTTCCATAAACTCCACATCATCAAGAAACTAGTACTAGACACTACTCTTCCAATGCAAACACCACTATTCCATACTTAAATTTAATGCTACTTATCTCACATGATGTCTTGGATGTTGTGTAGAAACCATGTCTCATGCAAGACATGGTTTCCTTCTCTTTCCTCATTTATTCACTTGCCATATCATTTTTCATCCTAGTTGGCATCTTATTTAATGCTATAGACACCATCCTAGTTATTGGGTTGGAAATGGCCTTAGAAACACGTAGCAAATAAATTTGGACACAAGCCCTCTAAATAAATACTCAGCATAGGATCCTTAGTAAATAAGTCAAACACACTTTGCTGAAAACCTACATTTTCTTTTAAATATCCTGTATCTCGTTGGTGCTTTAGCTATCGTGTTGTTTCTTAAGGAAGAAATTATATATCCAGTGAATGAACAGAAAAGCTAAGTTGGTTCATCTTCACTTAAAATGGTTGGATGCTTTGCATAGAGCTAGTTATTTGGTGAAGAGAATGCTTCTACCACTAGCAGTGGCGGATCTAACATGGGAGATGGTATTAAGGTCAAGGCAAATTTCTACAACAGAAGCTACGGTTAACGCAGATTCGAGGAAGAGAGCGTGGGTAGAGAGAGATGGGAAAGAGGATGTGCGGTAACGGATGCGGCGGAAGCAGCCGGACGAACGACGGCGACCCCTGCTCGCTCGCTCGCGCGATGGATGGGGATCGGCGCAGCAGGCGGCGGTGGCGGAGGATGTGCTCACCAGGATGCGGCGGAAGCAGCATGACGAACGACGGCGCCCTGCTCGCTCGCGCCTCGCAGGATGGATGGGGATCGGCGGCGGCGGCGGCGGCTGGCAGACT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.516987
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0305400.3 5 16269722 T C
Osa05LNT0305400.3 5 16268791 T A
Osa05LNT0305400.3 5 16269946 G A
Osa05LNT0305400.3 5 16270884 A G
Osa05LNT0305400.3 5 16273157 A G
Osa05LNT0305400.3 5 16273306 G T
Osa05LNT0305400.3 5 16269497 G A
Osa05LNT0305400.3 5 16270657 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
Osa05LNT0305400.3 osa-miR5528 Translation 3.5 8.952 1 21
Osa05LNT0305400.3 osa-miR160a-3p Cleavage 4.0 13.21 1 21
Osa05LNT0305400.3 osa-miR160b-3p Cleavage 4.0 13.21 1 21
Osa05LNT0305400.3 osa-miR160c-3p Cleavage 5.0 13.21 1 21
Osa05LNT0305400.3 osa-miR160d-3p Cleavage 4.5 13.21 1 21
Osa05LNT0305400.3 osa-miR395t Cleavage 4.5 19.052 1 21
Osa05LNT0305400.3 osa-miR395c Cleavage 4.5 19.052 1 21
Osa05LNT0305400.3 osa-miR395a Cleavage 4.5 19.052 1 21
Osa05LNT0305400.3 osa-miR395f Cleavage 4.0 19.052 1 21
Osa05LNT0305400.3 osa-miR159f Cleavage 4.5 18.606 1 21
Osa05LNT0305400.3 osa-miR319a-3p.2-3p Cleavage 4.5 18.695 1 20
Osa05LNT0305400.3 osa-miR319b Cleavage 4.5 18.695 1 20
Osa05LNT0305400.3 osa-miR418 Cleavage 4.5 16.749 1 21
Osa05LNT0305400.3 osa-miR815a Cleavage 4.0 12.319 1 21
Osa05LNT0305400.3 osa-miR815b Cleavage 4.0 12.319 1 21
Osa05LNT0305400.3 osa-miR815c Cleavage 4.0 12.319 1 21
Osa05LNT0305400.3 osa-miR1866-5p Cleavage 4.0 17.081 1 24
Osa05LNT0305400.3 osa-miR2055 Cleavage 4.0 14.045 1 21
Osa05LNT0305400.3 osa-miR2873a Translation 4.0 13.407 1 24
Osa05LNT0305400.3 osa-miR2923 Translation 4.5 11.627 1 22
Osa05LNT0305400.3 osa-miR2928 Cleavage 5.0 22.154 1 20
Osa05LNT0305400.3 osa-miR171d-5p Cleavage 5.0 12.924 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0305400.3 5 yl(t) Morphological trait Shoot/Seedling nan nan
Osa05LNT0305400.3 5 QKw5 Morphological trait Seed RG182 RG13
Osa05LNT0305400.3 5 qLTG-5 Resistance or Tolerance Cold tolerance RM249 RG13
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