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

>Osa09LNT0436700.1

GGATGAATGAATGAATTAGACTTTCTGGAGAACAATCTGATAAATTAACGAATTGAACCCGCGTAGTTTTCAGGCTATGAAAACTTTGCTGCGAAATTCAAACGAATGTTCCCCAACATAGATAGGAATTCCATGCAGACATTTTTGACAAATATTAGCATGCTGGGTGTATAAAATATATACTGCACTGAGCAAATCTTAAAAATCACTCTTTTCAAGACCTTACATAGTTGGACGCACCTGGACCTGCTGCAAAGAATTACTAGTGGGTTATATCTGCTGATTTGTTTTAGAACCCATACATTTACCTTTCCGTAGTACCTGGCAAGCTTGTGCAACACAAATTTGCAAACCTTCTCATCGAATTTGACTTGCAAATAAGCCTTTCGTGCCACCTATCTAATATGATATTAAGGATAAGAGCAGATGGCTTTGATATAGAGAGAACGCCATAACAATCAGCACACCTGCACATCAGAAGATAGTTTAGTGTGAAGTGCAGTGGAAAATAGCTCAAACAAAATCAACCCGCACAGAATCATGTGTAATTTTAAAATACTAGGACAAATCAATTAAGCATCCAATTGTGGCGTACCTTTACTATTTCATTAACTTATTAAAATGCTGAAGGCCAGAAATGCCAATATGGAACAATATAAACCCCTCACCAGCCACCAGACTAATGAGTACCCCTTTAGCCCCAGGGAAATAATAGGGGAATCCACAATACGTTACAACATCTTCAACCTTTCAAGCACATCGATTCAGGGGAATTACATCACATATGAGCATGGCAAGAAAGCCATGCTAAATCCATCTTAACAAAATATTTTTGTTATTACAATTTCCACATGTTGCTGAAGATGAATTGGCTAAAGCTATGTAACATGACGTGATTCAATCACTTACAAAATGCACGTTAGGATGTCATATGGGTACTTATTAGCATGCTAGCCTCCTAAGATCCCAGTCTTTCTTTTATGCTCTTAAGTGGAACAAAAAGACATATTGGTTCAATATAAGACCATTAGGCCTATAAGACTACTACTATACATATAATAGTGAAGTGACCCGTTTTAAAAATTAGGCTTATTCAAATACGATACATTTGTATCATGACTACATCAGCAAGAAATAGACAAACTATATTTGCACATAAAAATATTTTTAAGAAAAAATATAAAAACAAAAATAACTAGATTAAATTTTAGAAGACCACAGGTTTTGAGGCACGTGTAACACAAAACCTCAGATATTACGATTTGTTTCAAGGAAACCCAGGTTTTGAGGTATAGCATTTCAAGAAACCCCATGTTTATATCACATACTGATAATTCTATTATTATATATAATATTTTTAGTATATGTTTGCATTGGTATGCTCAAAATACATAACCATCCCGTGTACTTCATATTTTTCCTTACTTTTGCATTGTACGATTGAATAAACACAACCATACTAATAATGACATATTAACCGGTTTACTTATATAGATAAACATTAATCATATTACCATAATAATGCTTGTAAAAATGAGGCAAACATGCATATATATACTCACTAATATCTCGTTATTTTTTTGCAATTAATATGCATAAATATATTAGACAAATAACAATATAAGCTTAAACATGAGATTTCGTGGAACATTTTTCCCCAAAACCTAGGGTTCTTCATCACAAATTGTAATGCATGATGTTTTGTGTTATAAGTGTCGCAAAACCTGGGGTTTTTGTGAAATTTACTCAAATAACTACATTTTTGGCTATCATAGAAGATCCAATGGACCCGTATTGCATTGCGTTGGATGCACCGTCACCAAGATCTTGTTTCATAGGAACAAACAAAAAAATAGAACGATATTTTTCATTGAGACCACCTTCCCCAAGACAAAAGAGAGAACTAGGAAATGCTAGACTGTACGTGCTACAATCGTGTTCTGCCATCTCTAATCGCTAAGTAGTACGTAAGAAATGAAAGTATATATGCCCAGTTTTATAGGATACCGATGAAAATCTGAAGGTTAACTGAATGTAAGGATTTGGTCGTAAGGGCCTAGGCTACCAAATCATGACCTAACACAGAACATGAATAACAAATAGCTTGACAGAACAGATCAAAAAAACAAAATGCCAATAAAGGAACAAAACGGCGGCAGTCAAATGCAGAGAACAAGAAAATAATTTGTGACAAATGAAGCCTATCATCAAAACAATAAATTCCACAGTAGACCCAAACAGAGTGTCACCCATTACCATTAGTGTAGTCGATAAATTTTCTTCTGAAGAAGATGAGAAAAATACATATATTGTAATAATAAACACGTAGAAAACTTGAGCACAACGCCTCCTGCCATGGCTGATAACATGGATAGCCAGATGAAAGGGAGAACATCATCTCGTCGAACCCAAATTGTGAAACGTATGACCCTGCGACTTGTTGAGTAGGAGTGCATTGCCAAATACTGGAACTGAATCTCCCTTCTACGGTTAGCTCGGCAGAGAGGGGTAGACCGGGCGGGTAGTCCAGATGGCTTAGATCTAGTCTTCTCCGTTAAACTCATCACCGCAATACCATCGCCGGGAGCCGATTTGCGGCGGATGCAACCGCCGGCAACGGTGCCAGCCGAAGCCCCTGGCATCGTCTCGCCTATAGGGAGCTGAGCCAGCCACCGATTTCAACAGATCATCCTGATAATATCCTTGGCCGTGAGACCGAGTCAGCGCCGATAGACCGGCAAACTTCCGTCTACGGCCAAGTCCCAAGTCGATCTGGCTCCGGACGGATCATCTAGCCCGGGGTATGGATCATCCATGGATGGACGGCGACAAACGCGCGCGGCCACCGACGCACCCGGCGCCGGCCGCCGAGCCCATGTAGACGGCTGAGAGTTGACCGGCGCTCAGGACTGCCACCGGCACGCACAGGCGCCAAGGAACCCTCAAACCAGACGCTCGCCGGAGCGCTTACAAGCGCGGAGTCGACGTGCAGGTTTCGTCGGGCGGGCGAGCGGGCGGCGGCGGCGGTGAGGCGCGGCTAGGGCTCGCGGAGTCGCGAGAAGAGCACGGCGGCGGCTAGGAGTTGGAGACAGGGTTGGGGGTGGGGAACTGGGGATTCCGCGTCTATCGTTTC

Coding Potentia
Explanation CPC Score
noncoding -1.24243
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0436700.1 9 13141123 C T
Osa09LNT0436700.1 9 13143505 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0436700.1 DTM_#DNAt_MULE_japo_Os1030 Chr9 - 13145020 13145569 549
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0436700.1 osa-miR5542 Cleavage 5.0 15.462 1 21
Osa09LNT0436700.1 osa-miR1440b Cleavage 4.5 9.82 1 21
Osa09LNT0436700.1 osa-miR160a-5p Cleavage 5.0 21.549 1 21
Osa09LNT0436700.1 osa-miR160b-5p Cleavage 5.0 21.549 1 21
Osa09LNT0436700.1 osa-miR160c-5p Cleavage 5.0 21.549 1 21
Osa09LNT0436700.1 osa-miR160d-5p Cleavage 5.0 21.549 1 21
Osa09LNT0436700.1 osa-miR160e-5p Cleavage 5.0 21.549 1 21
Osa09LNT0436700.1 osa-miR171e-5p Cleavage 5.0 21.493 1 21
Osa09LNT0436700.1 osa-miR172a Translation 4.5 16.474 1 21
Osa09LNT0436700.1 osa-miR172d-3p Translation 4.5 16.474 1 21
Osa09LNT0436700.1 osa-miR810b.2 Translation 3.5 15.808 1 21
Osa09LNT0436700.1 osa-miR2055 Cleavage 5.0 9.315 1 21
Osa09LNT0436700.1 osa-miR2093-5p Cleavage 5.0 12.001 1 20
Osa09LNT0436700.1 osa-miR2099-5p Translation 5.0 18.136 1 22
Osa09LNT0436700.1 osa-miR2864.1 Translation 4.0 11.399 1 21
Osa09LNT0436700.1 osa-miR2866 Translation 5.0 13.902 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0436700.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
Osa09LNT0436700.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0436700.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0436700.1 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
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