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

>Osa09LNT0439300.1

GTAGAGGTAAGCTATTGTTTAATCTGAGGGGATTTCGCTTGGCATCTGTCAAACTAAGAAAAGTGCTTCCTGTTTCTTTTTTCTTGACATCTAGATAATGGATAAGAACAGAAAATGAGTCTAAAGCTACTTTAAAGCTAGCTAAACTGCTTATACTCTCTAGATCTGATCAACTGGAAACCTGACCAACCAGAGAAATGTTATTCTATGGTGGGCATTGAGCAAATGGAGCTTGATTGGAGCGAGCAGAAGTGCTACTTGTCCTTGTGTTCTGCAAGCTGGTCATCTTGATCTCCATTGTTTCTGGACATAGTTAACGGCTGCAGCTCCAGTTCCTGCCTGCGTGACCGAGGTGACCTGAGTATCCAAAATAAATGGCAGTTAGACACAAATTCAATCACGCACCGATGATTCATGGGATCTTTTGTTATCATGTTGTGCCTAGCAGCAAATTGCGAAATCTGAAGTCTATACTCTGCTGATGCTAGAATGAACAGCACAAAATTCTGAACATGAAACGTGCCTACACACACTCCTTACCTCTTCCGTAAACTGGATCTGTTTCCACCTGAGGAGAGCACGGTAGCAGGTGCAGACAAATATCCAGCATCATCTGACGATGAGGTGCTCGTCTTTTCACATTGCAGAAGAACATGGGCAAAATAAATTCTCCGAAAGTTTGTAGATGGAAAGGATAAAAAAAAAAGGATATGCAGATCCTGGTGAGCTGGTGAAAGTTTCAGAAAGAAATGTACTCACATTTTGATGAGACGCGGTCTTCTTCAGCTTACGTGTCTTCTTGTTGTGATTTTTTCCCTTGCCTTTGAGAGCACAGATGCATTTTAAGATGTAATACAGAAGAACACACCCAAGGGATAGCTCAATTGTTAAGGCTGTTCTCAACACTGAAAGTATTTGTAACACGGAGAAATGGTCAGTACAATTTGGTGGATGTAGACATCTAGTGCAGAAGGTTGTGCTAAACACAAAAACCACCAGCATGGACACTTACAAAGATCTCTTGACTTCACAGATTTCCTTATGAGTAGACGAATGGTCTTTATGGTGGACAATGGCGTCCCTGATTTCATTGAACAGTCTGGGTAGCATCCAAAGTATCCCAGGTCATTTACAATAATAACTAAGGTTGTTTCATTGCTTCGACCCTGAAAGAGAAACATAACCCATATTTTAGTCTGAACATTCTCCTAATCTCCTGTGGGGCATGAAATATACCATTTTAGTCTGAACACTTAGGTAATCATTCACAAAGTCAGGCACCAATTCAATCTTTCCAAAAAGCAGTTCATTTGGATTGTCTGAAAAGTTTAGCTTTCCTGAAGTGCAGTAACAGATATGCAATTACAAAGACACCTATGACTTATGCAACGGACTGCATAATTTACCTGGCCGAGGAACAACATATTCACTCAAGAAAGGAGACAAATAATTCATGGAATGAACTAATGAAGTGACCAGAGAAGATAAAATATTTACCTGGTAGAACAACCGCTGCATTGCATTGTTGCAATCAGAGACACTCCCACGGAACCTGATACCAGCTACTCTCAGGACTATGCGATCAGCACTGGAAGTCTGAAGGGGCTGCCAACAGTTGTTCCCTTCAATCTTCACCTCTGCAGTGGCGACGATACCAGCTGTCAAGGTTACCATGAGAGCTCCTTCATGAACTTCTAATGAGAGAACCAGCTGAAGATGGGACTTGTTCCCTGCAAAACGAATGAGAATAAAGCGAGCTAAGTTAATCTGAAAGGCCAAAGAACAACAGTTACATGTCAAAGTAAGCATGATATTCCTCATCTACCAATAATAGAAAGAGGTGATGAAGTACCTGGGAAACTCTGAAGATCTGGTTCAACAATGGAGGACTCAAATGGATCCCTTTGTTTGTCAAAGATTTGATATCCTTCAATTGATTTTTTCCCACCCAAGAAAATCGATTCTGGAGCTAATATAACTGGTGGATCGTTGATTGGCTCTACGAAAATGGGTACTTGAGCATCTTCTCTTCCACTCCTGCTCATGGCATAAATCTTTATAATATCATTTCCATAGAAGTCTTCGTTTCCGATATACTTAACAAATCGTAGCGCTCCATTTATTGCTTCGACTGTTCCGTTGAATATCAAATCTTTGCCATATCTATCTCCTGTGCTGATTGAAAGTACGTCATATGATGTCTGATGAAATTTCATTGGCATAGGAGCAAGAGACACATTTCCAGACTGCGCTTGTAGCATAACAGAGATATTTTCTGCTGCATCTGAATATGCTATCTTAATCCCTGGAAACCCACCGAATTGTGGGGCAATCGTGTCTTCAGTAGCATGTAGCTGTTGGGGTAAAGAAATAAACTGGGGTGGTCTGCAGAGAACTGATATGAACACTGTGCCGTATGCAATGTTGTCATGCTTGTCGAATATTATGTACCAAAATGTGTCATTTCCAAAGAATCCTTCGAAAGGTGTGTACCTAAATTTTTTTTGATTGTATTGTAGGACTGACCCATGAAGCGGCTTCAAAAAGGTAGGCACAAAGTTATCATGAATTCCTTGTTTTTTTTTTAAAAAAAAACAAGGTTATCATGAAATCGAATTGGTGAAATTAAGTAATGGCATGATGAAGTAACTGGAATATTACTCCGATCCACATATTAAAAGACTTTTTTTTGGCTAGATTTATAGTATATTTTAAGTTGGAATATTACTCCGATCCACATATTAAAAGACTTTTTTTGCTAGATTTGTAGTATATTATAAGTTGTGTTGTTAAAGTGTTAACATGTACAAGACTAATATATCGCATGAGAAAATTTTGTGGTTATCACTAAGAAGTTATAGATAGTTTTGGGGCTGAAAAGACGCGAATATTAGGGAATGACCTAATATCAAATAATTAGAAAGGGTATGGCTTCGAAAAGCTCACCACTTTGTGAAGCTAGCCGAAAGACCCTTGGGTGGTTCTTAGATAGTTTTGGGGCTGATCTGGGGAATTAGTTGACGGCATGGGCTTACCGGATAAAAATTAACTACAGCTTGGCCTCCTGCAATGTAGTCATTTGACAATACATCAAAGGAAACAGATTCATTCTCCCGTACTGAAATTATATCGTTTTGAACCGTGGAGAAGTCTTCATCTTGAACAACATGCACTTCGAATGGGCAAGGTTTCAGTTGTGCATCCTCAAACTGAATACAAATTCTATATAAACCGGTATTTTTCGCCACATAATAAGTAGTATACGATCCATCTTTGTTGTCAACAAACTCCCCTGCGGTGAAGCTTGGCGCATTCATAGGGGTTGTACTATCTGCAGAGGTTAGCTGAATCCTCAATTTTGATGCCAAGTGTATCATTGGATTCATGAATGGATCAACAAGTTGAACAACTACTTCATTGTGGACTGAAGTTTTGACTTTACGAACGAACGTGACAACTGTTGATAAATCGGTGCTAACTACACCTGTGGAAACTGTCATTTTATAGGGATTTCCACTGTTTATCACTATGTTCCCACACTGAACCCAAATTTCATACTCCCCAGCAAATTTAGGAGTATATGAAACATTAAAACTATTTGGTCGCATGTTTCCTGCAATAATTTTTTCCTGATGGCCAGTAGGTCCTCCACTGAAATGTCCTCCCACAAATGTACTGAAATGTCCTCCCACAAATGTTTCCTCATTTAATTCTCCTGGAGATATGGTTGAATTTACACTAGCACCATTTTTACTCAAAATCTGTACTTTCAGCCATGCGGATTCAATTGGGGAAGGATAGCTATAGTGATCCTGCAGGTAAACCATAAAATGTGACACTGAACCGGCAACTGAATGTGCTAAACCAGATCCATTAGCAAAACTGTTTGAACCATCGCAATACCCTACAAAAACATTATACACGTAGTCCATGTTGGAGATCTTTTGGTTCAGCTTAGGATCGAAAATTGTGAGAACAAACTCTCCAGGATCCACAGCTTTGAAAGAGAGCAGCCGAGTTCCATCGTCCACAACCTCAATCAGTAGATCTGCTACCGGGACAGACAAATTTGTGGCTCGTTTAACTATTCTAGCATCAAATGGATGGATATCTGGAACAGCATTTCCAAAATAATCCTTCTGATGTATGAAAATCTCCAGCTTGGAAAATATCTGCAATACATTAGTCCCATACTTCCAGCTGCATGTGCTTTTAGCTATATCAACAGGGCCTGGATTGACGGTCAGTAACAATGGCGAACCACGCAATGTGTTGTCATCGCTCTGAACCCGGACAAGGAATGCTCCAGCAACAACCGGAACAAACTCAAGGCTGATGCGTCCATCTTCCGCCCATCCATTGTACCGAAAATCCTTGAATTCCACGATGGCGCCATTGCTACGGGACACCGACACCTTCAAGTTGCCATTGCCGCCGGGCATGTCGGCCCCTCGCGCGACGCCGTTGCCGAACGCGTCCCTGAGAGCGACCGACACGGACGCCTTCGATCCGGCGACGCACG

Coding Potentia
Explanation CPC Score
noncoding -1.22445
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0439300.1 9 15411070 A T
Osa09LNT0439300.1 9 15414725 A G
Osa09LNT0439300.1 9 15408697 C T
Osa09LNT0439300.1 9 15409912 T C
Osa09LNT0439300.1 9 15411224 C T
Osa09LNT0439300.1 9 15411335 G A
Osa09LNT0439300.1 9 15411847 G A
Osa09LNT0439300.1 9 15412438 C T
Osa09LNT0439300.1 9 15412633 A C
Osa09LNT0439300.1 9 15412735 A G
Osa09LNT0439300.1 9 15412741 T A
Osa09LNT0439300.1 9 15413196 G C
Osa09LNT0439300.1 9 15414400 A C
Osa09LNT0439300.1 9 15414475 T G
Osa09LNT0439300.1 9 15414645 A G
Osa09LNT0439300.1 9 15414678 C T
Osa09LNT0439300.1 9 15414749 A T
Osa09LNT0439300.1 9 15414927 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0439300.1 DTM_#DNAt_MULE_japo_Os1030 Chr9 - 15413483 15414030 547
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0439300.1 osa-miR5791 Cleavage 3.5 11.667 1 21
Osa09LNT0439300.1 osa-miR5796 Translation 5.0 13.772 1 21
Osa09LNT0439300.1 osa-miR5798 Translation 4.5 17.297 1 21
Osa09LNT0439300.1 osa-miR5802 Translation 4.0 15.215 1 24
Osa09LNT0439300.1 osa-miR5814 Translation 5.0 14.202 1 24
Osa09LNT0439300.1 osa-miR5816 Translation 3.5 9.405 1 24
Osa09LNT0439300.1 osa-miR5816 Translation 4.0 17.248 1 24
Osa09LNT0439300.1 osa-miR7694-3p Cleavage 4.5 19.399 1 22
Osa09LNT0439300.1 osa-miR398a Cleavage 4.5 18.872 1 21
Osa09LNT0439300.1 osa-miR167h-3p Cleavage 5.0 16.747 1 21
Osa09LNT0439300.1 osa-miR171f-5p Cleavage 4.5 8.651 1 21
Osa09LNT0439300.1 osa-miR393b-3p Cleavage 5.0 19.551 1 21
Osa09LNT0439300.1 osa-miR816 Cleavage 4.0 12.393 1 20
Osa09LNT0439300.1 osa-miR810b.2 Translation 5.0 10.319 1 21
Osa09LNT0439300.1 osa-miR1860-5p Cleavage 5.0 23.215 1 21
Osa09LNT0439300.1 osa-miR1861d Cleavage 4.5 20.023 1 22
Osa09LNT0439300.1 osa-miR1861h Cleavage 4.0 20.023 1 22
Osa09LNT0439300.1 osa-miR1861j Cleavage 4.0 20.023 1 22
Osa09LNT0439300.1 osa-miR1866-5p Translation 4.5 11.168 1 24
Osa09LNT0439300.1 osa-miR1866-3p Cleavage 4.0 20.119 1 22
Osa09LNT0439300.1 osa-miR1874-5p Translation 5.0 19.309 1 24
Osa09LNT0439300.1 osa-miR1320-5p Translation 5.0 10.326 1 21
Osa09LNT0439300.1 osa-miR1320-5p Translation 5.0 13.454 1 21
Osa09LNT0439300.1 osa-miR2092-3p Translation 5.0 20.54 1 22
Osa09LNT0439300.1 osa-miR2121a Translation 4.5 15.695 1 24
Osa09LNT0439300.1 osa-miR2121b Translation 4.5 15.695 1 24
Osa09LNT0439300.1 osa-miR2870 Cleavage 4.0 14.791 1 21
Osa09LNT0439300.1 osa-miR2871a-3p Cleavage 2.5 14.184 1 21
Osa09LNT0439300.1 osa-miR2871b Cleavage 2.5 14.184 1 21
Osa09LNT0439300.1 osa-miR5071 Cleavage 5.0 20.461 1 21
Osa09LNT0439300.1 osa-miR5073 Translation 4.5 9.583 1 23
Osa09LNT0439300.1 osa-miR5147 Cleavage 5.0 19.591 1 21
Osa09LNT0439300.1 osa-miR5157a-5p Cleavage 5.0 16.924 1 24
Osa09LNT0439300.1 osa-miR5157b-5p Cleavage 5.0 16.924 1 24
Osa09LNT0439300.1 osa-miR5523 Translation 4.0 11.4 1 22
Osa09LNT0439300.1 osa-miR2275d Translation 4.0 13.472 1 22
Osa09LNT0439300.1 osa-miR2275d Cleavage 5.0 19.172 1 22
Osa09LNT0439300.1 osa-miR1319b Cleavage 5.0 14.549 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0439300.1 9 qSB-9 Resistance or Tolerance Sheath blight resistance C472 R2638
Osa09LNT0439300.1 9 nan Morphological trait Panicle/flower RM257 RM566
Osa09LNT0439300.1 9 rdw9 Resistance or Tolerance Drought tolerance R79 R2638
Osa09LNT0439300.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0439300.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
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