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

>Osa09LNT0437800.2

ACATCTTTAACACAAGTAACTGAGCTGTTACAAATTTCACAAGTAATCGAGATGTTACACCTTTATTGACCTGCCCTCTATCTTGTACAATTCTATATGGATACCAGAGGTAATCAAATCAGAAGAAATGAGGCACAGCACGGCGTCGAATAATCCGCCTTCGCTAGCAGCAAATGCACATTCTACAGGGACCAAGCCTTTTTCCGCCTTGAGATCACGGGGAGAAAGACACTGCAATTGGCATGCTTGGTGTCCAGCCCACACACGACAAGGTGGCCTGATCCTCTGTTTCTATTCTATGATTTCTATCATTCTAAGGCTACAACAATGTTAGTAAGTGACCGAACCAATTAAAGAATGGTTGGCTAAATGGCTACCTGTCTCGTTTCACCCCCATTTTGCTCAAAAAAAAATTACAGCGGGGATGAAACGGTGACGATTCTGCTTCAACGTAGGGTAGGGTGGAAGAGGGAGGCAGGAAAAGCCCTGTTATGATGAGGACCAGTCGTCGGGGACGGCGAGGAAGTACCTCGACATGGCCTTCCTGAACCTCTTCTTGTACTGGACCGGCGATATGACGGTGGGGGCCTCGTTCTTGGAGCCGCCCAGGATGCCGGAGGCCTTCACCCACGTCTCCAGCTGCTTGTCCCAGGTGTACTGCCGGAGGAAGTCGATGATGCCGATCACGAGCTCGTTCTTCCTCTCGTCTACGCCGACCAGAAGCGAGTAGTCCATGACGTCCAATGACGCAAGGAATGATGTATCGTTCCAGACAGCTCTTTCCATTCTTTGTTTTGCCTTGCTCCCCAAAAATATAGGATTTGTATGCTGTGCCTCTATGAGATTAGAATCTAAAAGTACTTTATTGTGGCCGGATGTATCAGAATTATAGCGTGACCGCACGGAACCCTTTAGGTCATAGACCCTAGATATTGTTCGTTGGAAGAAAATGTTCTCCATCACCATAAGATCCATCTTTACCTCACGCCCTCCTTTCAAGCCCTTAATATTAACCTGATAAAGTCCCATTATTTTAGCCAAACAAGTCGGGCTCCTAGAAGTTAGTGATTCTGCCAAGTGCCTGAAATAGTGAGGAGCAAATCCTATAAAAGAGTCCAGCTCTGTCTTGGTGACCTGTTTAATTATGAATCTCTCATCCATTGTCTTTGCAAAGTATACATTGCTTTTTCCACCTTGTGCACTCCATCTCTTACAACGACTTAGTGAGCGTATGTAATCAATATCACCTGGGCAGCATTTCTTTCTAAGAGCAGCAAACTGCCTTGCAAAATAACATGTCACAGAAAACTTTGTATTATCAGCAGAAAATGCTTCATCATCAAAAGAAAAACTGAAGTGGGTTCCTTTAAATTCTGAATGGCCTTCTTGTGGGAGAAAAGATTCCTCAAATTGGTTATTACTGGCCACAGCACAATTTACTGGATGATGAAAGCTGCTCTTCGTATCCATTTTATGTGTGATGTGTTCAATGTATTCTTGTGATGTCATGACATACGACACAATACTGGTTGGCTCATCATCATAGACAGCAACAACAACGCCACCTTCAAAGTCAATATGAGGCAGTAATAGTCGTGCCCCATCGCTCACCATATGAGCAGCAGACCTGATATACGTTGGCAAATGAGTAAGGACATTTAAGTTTCCTCTTTCCCTGGGAGATATGTGAGAAAAGGCCCTCCGCATGTTTGTCAGCGGATCTTTTACTAGGCTTGTCAAATCTCGAAAGGAATCAACTGACTTTGAGGACAAATGCAATGAAGCAGGCAATAATCCCGTTGATTCCCGCTGATGCAATCTGAATATAGAATCAAATGAATGGATGCGAACAGGGGGGATTGCTTTACTGTAACTTGGATTTTCATTGCCTTTGGTTGTACTCTCAGGGAGGTTGTTGTGTAATTCACAAGATCCACTCCATGCCATATCTATTTTATCAGATAAAATAGATGCAAGTGAGGGTAATCTCTCCACTGGTTCTGTCTTGATGGAATCTTTTGATAGACTCTGTGCTATTCCCGACACATCAAATTTGCTGAAAACCAAGTCAAGGCCTCCTATATCATGCACAAAACTATCCACCATACCAACTGGCAAATCTATCTCAGGCAAGATAATCTCAGTGTCCATGGAATGGCCCTCTCTAGATAGTAGAGATTTTCTTAAACTTCCTGAAGAACACTGTGGACAAGTAGAAGGCTCTTGATGCATTTCTCCGTGATTTGTAATTGCCTGGTGTAATTCAGCTTCCGAACCCTTTATTCTAGAAGCACGGCCATCTTTTGTTATTGAACTTATGTTACAAAGCCTGCAGTCCCAAATGTAAGCATCTAGGAGGAGACCACGTCTCAGACGGTTGAGCTCCAAAATATCAATACTTGATTTCATGGAATGGGTACTCCCCCTGATAACTGGTAGAAGCAAAGTCTCATATTCATTTCTTTCCATGTTAAGCAAATCCTTCATCTCAATGATCTGTCTTTCTATGCCAGTTTTTAATGATTCATCCATGGTTATGATACTCTTTTCAGTATTAGAAAGGAATCCATATACCTCCGCATGTAAGGATTCCATTTCACCAAATACCGCAACTGCCTCTCCTTTAACCCATTCTTGTGTACTATGGCAATTGAAATCTAGCATTGAGGGTGGCAGGTTAACAGATAAAGTAACCATAGGACTGTACTGGAAGACAGCTACCATATTTCCGTACCCATAGAAACGAAGGCAGTCCCTCTGGAGAGAGTGACCACAACTGGCAAGTCGGTTGGCAGTCGCATGATTCGAAAAGCTGAGCTCTAGGAATTTCCCAAATGATAGACCCCAAGCAGCATCGGACATGATTACTCTATGTGATGCGGGAGGCATTCCATCCTCGAGTTTGCATCTCGTGCATCTGTGCCACATCCATATCCTTCCATCATGTTCACCTGGTAATTTTTGAGATACAAGACGTCTAACACTGATTGTTAGGCTTCCATGCTGGTGCTTGTAGCACCTAACATGTGATTCTGAATGCTCCTTACATGACGGGCAGCAATATGCCTGGTCAAATAAGTCTTCTCGAAGGTATCTCCCAAGTGGCTTATCAAAGCTACCATAAAATTTGATGCGGAAGAGGTGAGAACGCTCGCATGCCAAGCTTTTTGGGATGCATGTGCTTGAGAATGAAACTAAGATGCTCTGATGGTTGTCAGTACCAGGGAAATAACCACCTGAAAGCTTGTTCTGGTCATTCAGGCCTCCAACATGAAAGTCATCTAGTGATATGGGGCACCCACAGTTTTCCAGATTATGTACTTCTCCAAGTATATTAGCCGAAACACCAACTGGGGATTGCAAAGAGTTGCACGGATCATAATATGGTGTCACACCCATACTACCAAGGTTGTTGCCCAAGGAAACTGAATGCACATTGCATAAAGCATTTGGATGGTGCGAGTGGAACGAATTGTCACCTTTAATATGATTGGCAGGGGATTCAACCTCCCTATGTTCAGATACTATTCCCTGGCTTTCCCCATCCAATGGTAAAAAAGTTGGCGGTCCAGAAATACCATTAAAGATCTGGCTGATAGAAGCATTGTGTGCATATTTTTCTTCTTCAGTTCTCAAACTAACAGGACTACCCTGATTAGCATAACAAGATGATAGGTGCTCTCTATTGGTTTGCATTTCTGGTGCACCTACAGAAGATGTTGAAGGAACTCTTGGAAGTGTTGCACCCTCGTCCGCAAAGAATGACGTTTCAAGGGAGAGATGATAAGCAGCAAAGACTGCAAGTTGCATTACTCGCTTAATTCTTTTTAATTCATCCCGGCAAGCTCCTCTGAGTAGAACCGTGCAACCCAAACGCTTCATACAGCCTTCAAAGAACATAAGTGTCTTAGTTGACTTTTTCTCTGAATGTTCTGTTGAGGATTCTAGAACTTTTTCCACCTTGAACGTGTCACAATGGCCTAGTCTTGCTGAGGCAATGTTGTCAATTGATGAGGCAATTTGACCACCCGTGCATCTTGATATCCTATCCAAAAGTGGCCTCTTCACATTCAGAACTAATGAAATATCTTTTGCTAAGAGCTCCTGAGCAAAAGAAGAGACACTTTTCTCAACAAGCAGCACATTAGGTCGTCTTGACTCGATCTTTCCAACAATCATTCTGAGATGTTCCTTTTCCTGTTCAAGTATAGTTCCTATCGAGGCTAGTTTATTAGAAACTTTCTGGTATTCAAGTGCCCCTCCTAAAATGAGCAATGTGGCATTCTGGTGCTCAGAGACCATGCGTTTGTGTTTTACATTCTTGGAGCAAACAATTCCTTTAACAAAATTGCTCTCACTTGGTTTCCCCGATGCTATGCATTTAATCTTCACGTAATCACTAGGATCCATGCTACCACCTTTCTTTGTATCAGGTTTCACAAAGTTAGCTGCTTGCCATGCCAAAGAGGACACTATCTCAAGCCAACCTTTTGATTCTTTGTCCCTGGCCAAACTAATAGCTTCCCCTGTTAACAACTGTGCAACTAGAGCTTGAAAATGCCTTAGCAAATCATTTTGAACATTCTCTATGTGAGATCCATTAACGGAACTATCAACACCAGCAAATTTATCAGCACTGAAGCAATTAGGCACAACAAAATTGCTGGAGTCACCATATTCATCGTCCTCATCATCAAATGCACATAATTTTGATTCAACGTCATCGCTCTCATCTTCAGGAGGTGGTGGGTACCAAATATCATCATCAAAATCAACAATACGGAATGATTTATGCTCCTCTTCACACCAGGAAGCTATGCTAGCACCGACATGCTCCCGAGCATCATCTGAGTCAGACATGGTTGTAGCACCATGATCAGAAGCATCATTCTGCCTAACCGTAGGGCTCTCTGATGGGCTTGGGGTTACTGATCTGTACATTGAGTTAGCAACACTAACACTAGAATCTGAATCTGAAGAGTCATGTGAGAAGTAAGTCCCTGGGGCAAAAAACTGGACCCTGGGTTCGTCAATCTCCTCATCTGCTCGCCTAATATCGCGGCAGGGAGGAGGCGAGCAGGGAGCGGCGATCGATCGATCGATCTTCAGCCAATGCGGACACGCCGCGAGCCGTGCGCCGACGAGGACGAGGAGGAAGAGAGCATGCTCCGGCGAGGCGACGAGGCGAGAGAGGTGTGAGGTTGGATGAGGAGGAGTGGACGTGGCGAGCGAGGCGGCGGCGGCGGGCGGTGGCTGTGGGGGAGAGAGAGGAGGCTTTGGCTTCTTATTATACGGG

Coding Potentia
Explanation CPC Score
noncoding -1.13469
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0437800.2 9 14110938 A G
Osa09LNT0437800.2 9 14110168 A G
Osa09LNT0437800.2 9 14113090 T C
Osa09LNT0437800.2 9 14113155 C T
Osa09LNT0437800.2 9 14113584 A C
Osa09LNT0437800.2 9 14113678 T C
Osa09LNT0437800.2 9 14113803 C T
Osa09LNT0437800.2 9 14114149 C T
Osa09LNT0437800.2 9 14114583 A G
Osa09LNT0437800.2 9 14115439 A G
Osa09LNT0437800.2 9 14116007 T C
Osa09LNT0437800.2 9 14116620 A G
Osa09LNT0437800.2 9 14118189 C G
Osa09LNT0437800.2 9 14111240 A G
Osa09LNT0437800.2 9 14111421 A G
Osa09LNT0437800.2 9 14111616 A C
Osa09LNT0437800.2 9 14110883 A G
Osa09LNT0437800.2 9 14110904 T C
Osa09LNT0437800.2 9 14110963 A C
Osa09LNT0437800.2 9 14111043 T C
Osa09LNT0437800.2 9 14111052 A G
Osa09LNT0437800.2 9 14111307 A G
Osa09LNT0437800.2 9 14111329 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0437800.2 DTM_#DNAt_MULE_japo_Os0222 Chr9 - 14110883 14111378 495
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0437800.2 osa-miR5529 Translation 4.5 17.459 1 21
Osa09LNT0437800.2 osa-miR5540 Cleavage 3.5 13.426 1 21
Osa09LNT0437800.2 osa-miR5806 Translation 5.0 14.841 1 21
Osa09LNT0437800.2 osa-miR5824 Cleavage 4.5 16.631 1 24
Osa09LNT0437800.2 osa-miR5824 Cleavage 5.0 17.974 1 24
Osa09LNT0437800.2 osa-miR1861o Cleavage 4.0 21.495 1 22
Osa09LNT0437800.2 osa-miR166a-5p Cleavage 4.5 22.335 1 21
Osa09LNT0437800.2 osa-miR166e-5p Cleavage 4.5 22.335 1 21
Osa09LNT0437800.2 osa-miR396a-3p Cleavage 4.5 12.13 1 20
Osa09LNT0437800.2 osa-miR396b-3p Cleavage 4.5 12.13 1 20
Osa09LNT0437800.2 osa-miR160f-3p Translation 4.0 13.066 1 21
Osa09LNT0437800.2 osa-miR160f-3p Translation 5.0 18.073 1 21
Osa09LNT0437800.2 osa-miR164c Translation 5.0 12.899 1 21
Osa09LNT0437800.2 osa-miR166l-5p Cleavage 3.0 22.335 1 21
Osa09LNT0437800.2 osa-miR167h-3p Cleavage 5.0 15.675 1 21
Osa09LNT0437800.2 osa-miR169d Cleavage 5.0 12.892 1 21
Osa09LNT0437800.2 osa-miR1847.1 Cleavage 3.5 17.792 1 21
Osa09LNT0437800.2 osa-miR1856 Cleavage 4.5 17.951 1 21
Osa09LNT0437800.2 osa-miR1861a Cleavage 4.0 21.495 1 22
Osa09LNT0437800.2 osa-miR1865-5p Translation 5.0 14.762 1 24
Osa09LNT0437800.2 osa-miR1865-5p Translation 4.0 23.05 1 24
Osa09LNT0437800.2 osa-miR2870 Cleavage 4.0 18.759 1 21
Osa09LNT0437800.2 osa-miR395x Translation 4.5 12.27 1 21
Osa09LNT0437800.2 osa-miR395x Cleavage 4.0 14.426 1 21
Osa09LNT0437800.2 osa-miR3979-5p Cleavage 4.0 22.428 1 20
Osa09LNT0437800.2 osa-miR5155 Cleavage 4.0 16.473 1 24
Osa09LNT0437800.2 osa-miR5487 Cleavage 4.0 13.505 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0437800.2 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
Osa09LNT0437800.2 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
Osa09LNT0437800.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0437800.2 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
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