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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa01LNT0057300.2

CAGCAAATAAAATTCGATTTACATTACACTACTTGTTAGTCAGATGTTTTTAAAGTTAAATCTTTAAATACATGCGTGTCTTACACTATGGAGTATATAACAAATAATGTTCAGCGAGGATTGATGCTAGGTACAACACCGCTGAGGAGGTTACTGCCGGAGACATCGGATGATGACATGTTGTAGTGATGGTGATCATCATTTCCAACCCCAGATGACGATGAAACCATCATCCTGGATCCCGACGATGGGGTGGCTGTGTTGCTAGGTTCCAAGGATAGTGAGGACATGCTCCCGGTGTCCGGTGTCATTTGCCATATCTTCTCCAGCTCCCTCATCACCTCCACTATGGACGGCCTTGCGTCCGTCTCGTCTCGGCAGCATCTCAGTGCCAGTGCAGCAAACTTCTCCACGCATTCTGCTGGGTACGATCCCATCCGGCTGTCAACCACTGACAATATCATCCCACTCTGATTGGCCGCAACAACCTCTCTAACTATATTTCTTCCATGAGAAATAGGTTGCATCCCTGTCAGCAGTTCCAGAAAAACAACACCAAGGCTGTACACGTCACTTTTGTCTGTCAGCTTATGAGTAAGGAAATACTCCGGATCAAGATAACCCGGGGTACCCTTTATAACAGTTGACACATGACCAGGAGCAATCCCCTCTGATTCTGGCTCTGGGGCAAGCCGAGAGAGACCAAAATCAGCAACTTTTGCGACAAACTTTGAGTCCAGTAAAATATTGCTTGCTTTGATGTCACGGTGAAATATTGGAGGGTCTGCTTCTGTGTGTAAATAGAGGATGCCTCGCGACGACCCCAGCGCAATTCGTAACCTCGTGGGAAAATTTAGGGGCTCTTTTGATCGAGCTGAAAGATGATCACGTAGAGTACCATTAGGCATAAACTCATATACCAGCATCTGCTCATCTTCTTCATCACAATAACCAAGCAATGAAACAAGGTTCCGGTGATGCAGCCTGGACAGCAATTCTATCTCTGTGAAGAACTCCTTCGAACCCTGAAGAGATCCCTGCTGCGCACGTTTTATTGCTACTATTGTTCCATCAGAGAGAATACCTCTGTACACTTTCCCATACCCTCCTTGACCAATTAGTGCTGAGTCACTAAAGTCGTTTGTACCATGTGACAGTTCTTGAAAACTGAAGTCTTTTACACCATCAATCTTCATTGGAATTCTTTTTGCAGAGCGTCTTTTTGAAGAATATCTTGAACGTCTTCTCAGTATAATGAGAGTAATGAGGGATGAAAGAAATGCTGCTGCAGCAAACGCTGCCACGACAATACCAACAATGGCACCTGTACTTAGGCTGGACTTTGCACGATCTGGAAATACTGGATAGCATAAGAAAATATAAGATTACTCTCTTGAAAAATTGTTAACAATTATGGAATTAAACTTGAACTGCATGGTACTGTAACTGAATCATTAGACTCACTATATCTTGACCATACACAAGTGCTTTTTGTTTAGTAGTAAATGTGCACAGTGTATTTTTCCTGTAGTGTAGGACTGTAAGGTGTTTTCTGTTAATTCATCTCTAGTATATCCAGAAACCACCCATGCATGCTTCTTGTTAAGTAGTATATGTGCAGAGTGTATTCCCTGTAGTATAGGGGCTTTCTTTCTGTAAAGCCATCTCTTGTATATCCAGGGATCCAGCCCCTATGGGTACATTGAAACACAAGTTACAAGTAATTGAAACTTCTGGATGATGGAAGAAATCAAGAAATCAATCCCAGCTACAGGCAACAACCAGCAAGTGTGGCGGTGTGGCCTGGCATGTCGTGATGCAAGAGTATACCACCTTCTGATGCAGTGATGCTTACATCTTACTCCCCTGATTCCAAATGTAAGATGTTATAGGACTTAGAGGCACTTTTCAATGTATAATAGTTCCTCTTATTCCAAATTCCTCTTATGCTAATTAAGTTCTACCACTCATGTACAAATGAGGTATCATTTTAAATGTATAATAGTTGCAGGGCAACAAGGTCATTTGAACAGCTTTCTTAATTCATGTCAACCACTCTAAAACGACCTGACTTTGGAAACAGAGGGTTGATACAAATTATTAGGGAATAGGGTATCTGACACATCAGTAAGCATCTACTATTAATGGGGACAAATGTCCTCCTCAAGCTATGTGTAAATGGTGAATTTGGTTTCTCTACATTATAAGGTCCAAATCAGCCATCCTAGTCTGAAAACTTATTATTCAGTTTACCTCATCCCTTATATCGCCCACTGTCCCAATGGCATCTGGACCAGGAGCAACCTTGTCATTAGGAGTTTGGGACAATGAGAAATTTTGTAAACTTTTTGTGGCATATAAGAAATAAAACTTTCTTTTAGATGGATGGATAAAAAAGAAAGTAAAAGAATTGTCATGATTCACCACTCCTTTGGGTGGTCCTTCAGGATTTGTATGAGAACCTCGTTGAAATGTGAATACTAAACCAAATGTACAATGATATGGGAAATCCTGAAATGCCAATGAATGAATGGAAATTCATTGACTCTCTGAATTGAATTTTGTGAGTCCCTAAACTTAGATTAGCTAGGCAGGGTATTAAATTTCATTGGTTGTTCCTGTTAAGTTCTGACTAGACATTACACAGTGGAAATAGTGCACCCATTACAACCGACATCATTTTTCATAACTTGGTTACTTAGATCAAACCAACTGTTTTCACATACTTATTCTCACAGTTACTGGTCATTTGCATGTTAACTACCATAGACATCCTAATCCTGGTGAGATCCAGAACTATACTTGAAATCAAATATTGAATATTTAAAACCCCTACAAATCAGATAAATGCCAATACAAGAATAAGAAGGAAATGTATAGAGTCAATATAGCATACAATTGTTATACCACCCTGGATTGAAGTTGAGGAGCTCATAGGGCCCGAATATATCAGAGTCTGGAATCAGCCAGCCTGTGAACATTCCTCTCAGTCTTAACACCTCGCTCTTATTAAAATAAGCAGTGTTATTTGGAAACAGTTTCAGATTCATCTTCACCCGTGGGCCTTCTTCCCACATAAATTGAGAAACTTCTAATTGGTAAGAAGACAATGAAAGTCCAGATGACAAGTACTGTTGAAACTGTCCTTCATATGGAACAAAATCCCAAAATCCAGGACTCTTTAGCCGGTAATCAACATAAAGTGGAATAGCACATATACATCGTATTGGTGACATCAGTATGTTTTCAAACGGAAGGTCAGTAGAGCATGGCGGACAAACTGTGGCATTACTTGCAGAACCGTCAGGCACAATAACTGGCACTGATTGACAGTACTGAGTAATGTTCAGTTGATTTGGAGATGTGCAGATGGGGTTTCCAGATAACAGGATGGTAACATTGGCAGGTGGTGAAAGAGGATTTGATAGATTGGTTAGAGAATTGTTCTGGAAATCCAATATAAGACTTCTATTTCCACTGAAATCAATATTCCGCCAGACATCTGATGGAACAGAACCATCCAAATTGTTATTGTCCAATGACAGTCTTTGTAGATTGGGAAGGCCAGAGAAACTTCCAGGAATTGATCCATTTAGAAGATTGTGGGAAAGATCTATTGTGGTTATGTTGCTTGCTGGTCGGCCAGATGGTATTGAACCCCTTAACTGATTCCAACTAAGATCCAGATAGCCAAGTTGGGGTATTCCACTGACATCAGGAACAGGTCCTTCCAAGCTGCAGTTCCTCAAACTCAGTTTCAGAAGTGTGGTGATATTGCCATAAGATGAAGGAATTGAGGTTCCTGAGAAATTATTGTTGTCAAGCTGGATGATAAGTAGTTTTGGTAACTTCGATAACTCTGGAGGAAGATAGCCCGACAAGTTATTGTTATCCAACAATAAGTGAACAAGTGAAGGTAATCTGGATAGTTCAGGTGGAATTTGACCACTTAATGAATTGTTGTTCATATGAAAGTGCTTTGTTTTGTTCAGATTAGCAAATGATTTAGGTATGGGTCCAGATATGTAGTTCTGGTCGATCTGAATCCTATCCAGATTAGGAAGGAAACCAATCTCCTCTGGTAGAGAACCAGTAAGCTGGTTTCCATTTAAGAGCAGTAATTTCAGAGAAGTGATGTTGCCAACCTCCTTAGGTATGCTGCCACTGATGTTATTCCACATAAAATCCATTATTTGCATGTGAGATAGCCGACCAAGCTCAGCAGCTAAAGATCCAGATAAATTCAATTTTAGAAGTTGCAATTCTAATACATGGAGATATCCATCACTTGCTGTTTCATTGTAACAGTGAACATAAGACCAATTTCCCATGCACGGATCTCCACGGTTCCAGTTGTTTAGACGTCCTTGCGGATCTATCAGATTGCCTTTGATAGCTTTCAGAGCATCAACTTCCCAAGGTGCAGTGATCTGTGCTTCTGTTCTTTGCACCAAGTAGAACATGAAGATAATGGAGCAAAGATAGAAGAGTCGAGACTGCCGCATGATGCTACTACACAGAAAATTTGCTCAGTTTGGCAGGATATTGAGAATTCACCGATGTAGTTTCCCTTTGATAGCATAATCCAGTCCCAGCTGGTAGGAGGCAGCAGAAAGAAAGAATCAATCGATCCGCCACACCAATGGAGGATTGTTGTAGAAAAGGACAAACCTGAGTAGTATTAGTCAAGCAGAGATAATAATCAACCGAATATTAACTATATAATGGGGATTAAGTTGGGCTTGGCCGCTTGGGTGTGAAAATGAGCGAGCAAAGTACAGTATAATATTATAAATAAAGCCATGAAGAGGTAGGAAAGGGATAGGGGGAAGTAGTACACTACATCGAACTGAATCGATTGACCTCTTCCAGTTTCCTACCAGCTGCCACAACGCAAACTCTTAAATCTCAAATCCCAAATCCTGAATAATTTCTGCTTTTCGCCACGGCCCACGGGTGACACGAGCAGTGATGACAAGAACATTGAAAAGGTGATGGAAAATGTCGTAGTAAATTCGGGGTTTGGTGATGGTGGACTTGGCAACGCCCCTCTCCATCCATCCATCCATCAACCAATCTGTCTCCCTCTGACCTCAGCAGCGCACGCAAATTCATTGAATTCGACTTCGCCACCCCACCTATCTATACGGAAATATCTATCGATCTATATCAACAATATTAAAGGCAGACGACTTCCAGATTGGATTCTTGGACCAAGTAAAACAACAGCAAGAATTGAGGCAGACGGAGGAGGAAGAAGAAGAAAGGGTCAAGCCTTCTGTAGCCAAGGAGGCCATCCTCTTCCTGTAGCCACCAGCCGCCATCCCCATGCTTCGCAAGCTGCCGCAACCATATCAGATTTCTCCCCGCGCTGTAGCGTCGCCGCGACGCTTCCGATCCCCCAATTATTTTCTTCTCTCCGCTCAACACAAAACCGCGTGTTTATATTTTCTGCATTGAATGAATGTGCTACAGTGATTTGCCGTTAATGTTGATGGTTTCGATTTAAAACTGATTTTAACGGAATTTTGTTTGGCTTATATAGGTGGGGGGAGAAATGAACTTTATATACTTCGACAGTAGAGCGGGC

Coding Potentia
Explanation CPC Score
noncoding -1.03774
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0057300.2 1 42336527 G A
Osa01LNT0057300.2 1 42339165 C A
Osa01LNT0057300.2 1 42339244 G A
Osa01LNT0057300.2 1 42339408 T C
Osa01LNT0057300.2 1 42339835 T C
Osa01LNT0057300.2 1 42339964 T C
Osa01LNT0057300.2 1 42340608 G T
Osa01LNT0057300.2 1 42342774 T A
Osa01LNT0057300.2 1 42343202 T G
Osa01LNT0057300.2 1 42343714 T C
Osa01LNT0057300.2 1 42344361 T A
Osa01LNT0057300.2 1 42345095 A G
Osa01LNT0057300.2 1 42345570 C T
Osa01LNT0057300.2 1 42345817 T G
Osa01LNT0057300.2 1 42346001 A G
Osa01LNT0057300.2 1 42347259 C T
Osa01LNT0057300.2 1 42347343 T C
Osa01LNT0057300.2 1 42348946 G A
Osa01LNT0057300.2 1 42348863 T A
Osa01LNT0057300.2 1 42349458 T G
Osa01LNT0057300.2 1 42348069 C A
Osa01LNT0057300.2 1 42336359 C T
Osa01LNT0057300.2 1 42339557 T C
Osa01LNT0057300.2 1 42346400 A G
Osa01LNT0057300.2 1 42343544 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0057300.2 DTM_#DNAt_MULE_japo_Os0312 Chr1 - 42337293 42337679 386
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0057300.2 osa-miR5541 Cleavage 3.5 12.448 1 21
Osa01LNT0057300.2 osa-miR5789 Translation 5.0 19.919 1 21
Osa01LNT0057300.2 osa-miR5825 Translation 4.5 16.431 1 24
Osa01LNT0057300.2 osa-miR6247 Translation 5.0 15.491 1 21
Osa01LNT0057300.2 osa-miR156a Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156b-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156c-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156d Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156e Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156f-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156g-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156h-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156i Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR156j-5p Cleavage 5.0 17.037 1 20
Osa01LNT0057300.2 osa-miR396c-3p Translation 3.5 12.497 1 21
Osa01LNT0057300.2 osa-miR396c-3p Cleavage 5.0 16.084 1 21
Osa01LNT0057300.2 osa-miR164d Translation 4.5 12.307 1 21
Osa01LNT0057300.2 osa-miR415 Cleavage 4.5 22.29 1 21
Osa01LNT0057300.2 osa-miR417 Cleavage 5.0 10.501 1 21
Osa01LNT0057300.2 osa-miR818a Cleavage 4.5 21.461 1 22
Osa01LNT0057300.2 osa-miR818b Cleavage 4.5 21.461 1 22
Osa01LNT0057300.2 osa-miR818c Cleavage 4.5 21.461 1 22
Osa01LNT0057300.2 osa-miR818d Cleavage 4.5 21.461 1 22
Osa01LNT0057300.2 osa-miR818e Cleavage 4.5 21.461 1 22
Osa01LNT0057300.2 osa-miR1438 Cleavage 3.5 11.835 1 22
Osa01LNT0057300.2 osa-miR1877 Cleavage 4.5 9.873 1 24
Osa01LNT0057300.2 osa-miR1882e-3p Translation 4.0 14.291 1 24
Osa01LNT0057300.2 osa-miR1320-3p Cleavage 4.5 11.841 1 21
Osa01LNT0057300.2 osa-miR2101-3p Cleavage 5.0 17.263 1 22
Osa01LNT0057300.2 osa-miR2275a Translation 3.5 15.122 1 22
Osa01LNT0057300.2 osa-miR2275a Cleavage 5.0 20.422 1 22
Osa01LNT0057300.2 osa-miR2275b Translation 3.5 15.122 1 22
Osa01LNT0057300.2 osa-miR2275b Cleavage 5.0 20.422 1 22
Osa01LNT0057300.2 osa-miR2875 Translation 5.0 11.326 1 24
Osa01LNT0057300.2 osa-miR2875 Translation 5.0 11.585 1 24
Osa01LNT0057300.2 osa-miR5160 Cleavage 5.0 5.903 1 22
Osa01LNT0057300.2 osa-miR5337a Cleavage 4.0 15.562 1 21
Osa01LNT0057300.2 osa-miR5337a Cleavage 5.0 20.303 1 21
Osa01LNT0057300.2 osa-miR5338 Cleavage 4.5 15.29 1 21
Osa01LNT0057300.2 osa-miR5487 Cleavage 4.5 15.525 1 21
Osa01LNT0057300.2 osa-miR5509 Cleavage 4.5 20.707 1 21
Osa01LNT0057300.2 osa-miR5521 Cleavage 3.5 20.047 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0057300.2 1 nan Morphological trait Seed RZ730 RZ801
Osa01LNT0057300.2 1 tn1-4 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0057300.2 1 fll1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0057300.2 1 ph1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ801 RG323
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other disease resistance RG109 RG236
Osa01LNT0057300.2 1 sd1 Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Morphological trait Root RZ730 RZ801
Osa01LNT0057300.2 1 PLFDH Morphological trait Panicle/flower RG323 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ801 RG323
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RZ14 R117
Osa01LNT0057300.2 1 ph1.2 Resistance or Tolerance Drought tolerance RM104 RZ801
Osa01LNT0057300.2 1 Fh1-2 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0057300.2 1 PNF(DH)1 Morphological trait Culm/leaf RG323 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RZ730 RG810
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RG810 RZ730
Osa01LNT0057300.2 1 qNOP-1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0057300.2 1 qPHT-1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0057300.2 1 qPL-1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Drought tolerance RZ14 R117
Osa01LNT0057300.2 1 qPH1-1 Morphological trait Shoot/Seedling C86 RG236
Osa01LNT0057300.2 1 pl1.1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0057300.2 1 qPHT1-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0057300.2 1 sd-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0057300.2 1 qRIE 1 Resistance or Tolerance Submergency tolerance C86 G54
Osa01LNT0057300.2 1 nan Morphological trait Culm/leaf RZ801 RZ14
Osa01LNT0057300.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0057300.2 1 rrw1b Resistance or Tolerance Other soil stress tolerance C86 RG236
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ801 RG323
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ801 RG323
Osa01LNT0057300.2 1 nan Morphological trait Root RM1387 RM1067
Osa01LNT0057300.2 1 qRNd1 Resistance or Tolerance Other soil stress tolerance RG236 C86
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 ph1 Morphological trait Dwarf RG236 C547
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0057300.2 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
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