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

>Osa01LNT0046100.1

CCGGCACAAACATAAGAAGACTTTGGGAAACAGTGTGCAGCGAATAGATATAGCACCAATTATAAGAGTATAAGTTCTGGCGATATTTGATTAGAACGTGCATATCGTACAGACACCACATACTATTTATACGAATTCATTTATCGTTCTGCTAGCCACTAGGGCTCGCAAGCCTGTAAGACGTAGAAGTAATGTCATTTGGTCTAATGGCTTGCACAAAAGAACACATCCCCTATTTATATTCCCACTGCAAAATACATTGGGCAAAATATGTGAGCATTAGTCTTGCTTGATCAGGGACAGGAGTATACGCCTTGGCATGCCAGGTGCAAAAGACCGCTTTGGTGGGGTGATATTATATGGAGCCCTCAAGTCATTTTGGGGGCTGCGGGGGCAGTTTGTCTACGAACAGCGCACGCACAACTGATGCTTTCTGACAATCATGTTCACGAGGAGATGAACCTTCCTGAGCAAGATCCTCATCAATTACAGAAGATTTATGTTTTTTGTCTGGTTGTGCCATAGCCAGGACCTCTGAAGTAGGCGGTGTTGTCCCATGCTGATCATCACGGCTATCAGTTGTGGCCTTTGGATCTGGAAGCACCAGTGGTGTAGAAGGTGTCATAGATTGGAGAGAAGAGCCAATTATCGTGTGCGGTTCAATTGCATCAGCTGGTGATGAGCCATGTTGAGAAGATGCCACAGAAGCATCATGGCTGGGCAGAGTACTTGTGTGGGCTGCATCTAGTGAGGCTAGCATAAGGGAATCCACTTGGTAAGATATCCGATTTCTTTGCAATGAGCCACGTGACACACTAGTTCTAATGACATATTGTTTTCCAAAAACTGCTTTGATTTCTGATGGAACTATATCTCGTGCTCCTTGGACAGATGCAACCAGGTTAAGAAAAGGGATGCCAATCAACTGGTAGCCAATTTCTCCAAAGAAGGTAAACTCAGCTGTTTTGGCGTCATGGTTCGTCTAATGGGTCGACACCTATGATAGCCACTCTGTACCTTGTTTCAATTGCATTAGTGATGCACCTCGAGCATTTATATGTGTTCCCTTCTCTACCTGCTCCTCTCTTACTGGTGTTGCATGCTATGTACCACCAGGCTTCAGCAGGGACTAAATCCTTGATGGCTATCTTGACAATATAGCTGTTGCCCAAGGCTTCGTGGGGATTAAGGTCACAGATATCAAAAACTTTTACATGCACAGCTTCTTTCTGACCAAAGTTCGGCTCTATTGCCCTTACCACCTGTGGGTTACCATGGAGGCTGCTTATGAGAGAAATTGTTTCCTAGATTGGTGCATTGGGATACCACCTACAAACAGTGCTACCTTGTAGGGCTAGCTGGTCGTCTCGGAATTTAACAGTTAATCCAACAAACAATATAACAACAGGTCCATGGTCTGGTTGCTGCTGTAAGTTTTCAGCGTGGAACTGTGTAGCATGGGCACCCCACAATGCAACGACAGCAGTTTCGCTTCCATTGGTTATGTGGACATTAAGCACCGCTTTCATAACACCTCCACAAGAAACAGTTTGCACTGGTCCAATGGCTGTCATTATACCTATAGCATCTGAAAGAATATCTTTCCTGTAAGCACGACCTCTGAGTTCATCAAAAGAAAGAACCTTGTAAGCATGAGATGGGAATGTGGATGGTGCCTCAGTGTCTTCTCTAACGGTTGTGTGGGCAGTGAATTTTGCCATGACCATCCGATCAATAGGCCTGTACTGGGGGCGCGCCTCAGCAACTTCGAAGTACTTGATGTAATACACAGCATCCTCCTTCAGCAAAGGCTTGAATTGAGAAACATGACGTCCTGGGATCTGCTCATCAAGCAGGACTAAATCAAGTCGCAGAATCTTGTCAGGTTCATTTGCTGTAGTGAACTGCGAGAAGCGCGTGACCCGCACTCGGACTTGCCAATGGTGTGATTCCTGTGTCACATTCCTTAGCATAGTGTAATCCATCTGCAACACATAAAGAAGGCATTACATAGGTTAGAGGGAAACTATAATAATAATAATACTTTGCATGATATGAAGATATAAAGTCCTAATTGTTGAAGGAACTGTGGTGCAGGATATATCTTTTTCTTTTTCGAGGTGGGAAATGTTTCCCAACTGACAGTGTTTCAAGCAGGCATGTTTAAAAGCAACTGATTGCATCCAAGAGAAGAATATGCAAAAATAAGAAAGAACAATTAATAAGCAGATATGGAAGACACTGCAACAATCAACTGGTCAAATAGGAAGAACACAAGTATGAACAACAACTCATTGAAGGGTAAAAAGAAAGCAGTAACAAATAGCGAAAACCAAAAATATGGATAGTCATTGTGGATAGAACACTGTATGACCATGAGTTCTTGCTTAAGTTACACAAGCAAACAGTAACACGGAGAAATGGGATCATAGAAGAAACAGGTGAACAAAAGGAGCAAAGTTTCCTAGCCGCAGTCACAGTGACAAACTGACAATAAGATTAATCTATAGCAACGATAATATTTCAGTGTAGACGATGTTCCTGGTAGTGGAACAAGGCTTGCCATCATCATCCTCTATCAACAACTTGAGGCCTTGCTTCGATGTAGCGCGCGAAACAGCGACATATAGCTGACCATGTGTGAAGACAGGGTTTCTGAGGTATACACCAACATTCCCCAAAGTTTGCCCTTGGCATTTGTTTATTGTCATTGCATAACATAGCCTAATTGGGAACTGCCTTCGCTGGAGCGTGAAAGGCCACTTTGGACTGTTCCCACTTAGGACAATCCATGGAATACAGACCAGCTGGCCAATATTTGTGCCAGTCATGATTTTGGACTCGAAAACATAATCACTGAGTCGGATGACCATCAATCTTGTCTCATTGCAAAGGCCGAGTGATTGGTTAATGTTGCGAAGCAGGACTACAGCTGAACCAATTTTGAGGGATATGCGATGTTCCTGGAAATTGTTTATGGATATTGAGTTTAGAAATTCTATGGGGTACAATAGATCAAAATCTACAGGCTTTTCAAGTGTATTTGAAATAGTGTCGCTGCTAAGATAGTCCTTTGCATCCCCAGGCACTTTAGCAAGCATATTATCATTAATCTCATCAACAACTGTATTGACAGGACAGACAATTGCACGCTGAGAAAGGTAAGGAATGCAGTCATAGTTCAATTCAAAATCTGGGTACACAGCATCAATTATAGCTGTAATCTTGTCACCGCAGGGAGTAAGCAGCAACTCCTTAGGTATCTCTATCCATGTCCTCTCAACCTCACCTTGTCTTTTGTTCATGGGAGCACGACCCTCACCAATGTCAAGAACCCATTTAGCAAACTCTGCCAATTCACCCCTGGCTTGCTGCGACAGGGATGGATTATGTAGCCTCATGTTAGTGGTAAGGTGTAAGACTTCAACATGCTTCCATAGTGCAGACCTAACCAGCGAAGCATCTACCACATCAGCTCTTGTACCTTTCTCAATCACCGGTAAGACTTGCCTAAAATCACCACCAAGTAAAATGGGTTTACCTCCAAAAGGCTTATATTCATTAGCTGGTTCATCAGCGGATTGAATATCTCGTAGAGTTCTATCCAATGCCTCAAAGCACAGCTTGTGTGTCATAGGCGCCTCATCCCATATAATCAATGATGCTTTCCTAATAAGATCTCCTAGGATTGTCCCTCTACGAATAGCACACATCGACCGATCATGTATATCTATAGGTATCCGAAACCATGAATGAGCAATCCTTCCACCAGGCATGAGTAGAGCTGCAACCCCAGAAGAGGCAACTGCAAGAACAATTTCACCTCTTGATCTCAGGTTTGCCATAATAGCATTCCACAAGAATGTCTTCCCCGTTCCACCATGTCCAGATATAAAAAAAAATACACTTTTCGTGATGGTCTATCCTGTCAAAAATCTTGTCATATATCATCTTCTGGTCATTGTTCAAGCTGGCATACATGGACAAAGATTCTTGATGGAGGCTATGTTGGTTAAAGCTAAGATCTTCTAAGATAAGCCTGTTTGCTGCACTGGATCCTGAACAATCAACTGGTGTTGGCAAATTGTATGATGAGATTGATAAGCCATTATTTGAGAACATGGCATCCAACTCTTTGAGCAAGGTATCCTGCAACATAACTTCTGGAATAGCTGTGCGCTGTACTCCAAGAGCTTTGGTTAACTTGTAAGCAAAATCATCTACCATGTATCTCCAGTACTTATCAAACAAAACCCTAACATCACCTACATCACAGTGTGCTAGTACAGTCATGAAAAGGTTCCTGAGCTGGTATGAAGTAGCCCAGATAACTGCCTCCTCAAAGAGGTGATCCCATTCAGCGTCATCACCAATGAGACCACGTGCCTGACAGGCTTCACGATAGGTGCCATACAGCACACCTTCATATGTCCTAATATCTTCAAAACTCATACATCCTCGAACTACCATGAGCAACATTCTAAGGTAGAACGGCTCCCAGTACTTGGATGGATGTGCCTTAATCTCCCTATCTTGGTTCCTCTTTTACGCTTTGTCCAAACTTTCTTCTCAGGATCCCAGCTAAACTTGGTAGGAAATTCACAATAGGTGAGATCCCTGGCAAAGATGTGACGTTGGTTGGTAGCAACCATTCAGTAAGCATTGTTCTAGAGGAATCAGGGTCTTCTATGACCTCTTCAAGGTCAGCTCCATCATGGTATGTCACGAACTGCATGCTCGGCAAGTGCACAATGAGGCGTTCAACAGAAGGACTCCTTCCATGGATCTCAAAACCATATAATCTCCAGAATGATTCACAAGTTGATAGGTATCTGGATTTGATGTGTTGCATAACCTCATCTATGCCTCCATTGCTAGCAGTATGAGCCTCTGTCTTTTCTGAAGTCCTGTGGCTGAAAACGAACATAGTCGAATCACTTCCCTTATTTATATACTTAAAAAGGTACTTGATAAGGTATGTTTTATTGCACCATTCCACATTGATATGAGCTTGGAATTTCTTCAGAAGAGCTGGATTATAAGGGACAACCCACCGGTTATCTAGTGAAACACCATTCTTCACCACATAGCAGCCATCATTGCGTCATCGATAAATAGGATATCCATCATCATCTATGGTAGTAACATCACAGAACTGTTTTGGATAGCCCTTTGAACACCGACCATCCTTCATGCAAGGGCTGCTTGGATTGTGCTCACCACATGGGCCATGTATCATGAATTCATCAACAAGACCAACCCACACCTATCAGCTGTTATATCTGGTATCTCAGCACAGATTAGGTTGTCAATGAATGCAGGTGAAGGATCTTCAGATTGAGCTGTGAGCCATGTTAATGTGTGGGAATGCGGCAATCCTCTTTTTTGGAACTCAACAGTGTACACAACAGCTTTTATGGGACCGAAGGCTTCTCCATTCTTAATAGATGTGATGTACTCATCTAGCTTCATATGGTAAACACGTGTGACCATATCACTTCTATCACTTGGTTTTTGCCCTGCCTCAAAACGAATAGCTTCAATAATCTCTGGCCATTTAGAATTGCAGGTGAAAGTTGAGAATATTTGAGGAGGACCGTAAGAACGGCAGATTGCCATTGAATCATGGTAGTTTTGAACCATGTATCGCCTTCCTCCTATGAAACTTGATGGCAAAATTACTTGGTGCCAACATCCTTTCCATCACTGTCTCCCCTAGCAACAGCATCAGATATACCTTGATGTGTCTCAGAGCGAAGTTTTTTCTGGTTGAGGGCATGGTATATGAGTCGAGATGTCTCTATACATGAGAAAGCATTCACAGCGAGCTGATCAGAAAGCCTACCACAACAGGTGAATGGATTGGGCTCATCCTTTCGATAGTGGGACTCGTACCGATAAAATTCAAGCATCGATGCTTCGTCGTGACTACCGGGTGGCTGATCATCTACCTCTCTAAGCTTGATACCAGTATGAAAACCCACATCACCATATGGGAATAGAAGCGGGTACTGCAATGACATAAGGGCTGGATGAATAGGTGACAACTGACATAACTCACCTGAATGCTTCTGCACAATGACATCAAACTTTGATACCTCACAAGATGCACTAGGTATAATCAGTGCTGCCAACTCAGAGGTGGTGGGAAGGCTGTAACGGTCACTCTGAGAATGGCCTGACCCAATGAGCTTGATAGCAATCTCAGGAGCACTTGAAGAAAGCAGCTTGTTTCGAGCAAGACGGAACTGCTGCACAAGAGGATTGAACTGATCAAGCATCGAGATAAGCTCTTGCACAATAACAGGATCAGGGACATCCCCAGGATTATCAGTGTGATCAAAAATATTAAGCCTATTCTGGAGCTCATTGGCGGTGTCATATATGTACAGCTGGGCGAATTCCGGACGTTGTCCAGGAGCAGGAACCAGAGAACCAATTCTGTGATGGACAACACCATTGATATGAAAACATAAGGCCCCGGACCAGTGTTTATGCTCCTATCAATGTTAGCCCCAAGCGATGTGAATGCAAATAATGAATTATATTGCCTGATGAGTCGCATGAAAGAGTTGGAATGGGCACCGCCATCAAAACGAATCAAGTCTTGTAAGATAGGAGGAAAAGGCTTGGGTGCGGGTAAGGAGATCTTTCCACCACGACAACACAGATTGTATGCAATCCTCTTGGCTCTGTGCGAGCTCTGGCTAACAACCCTTTCTTGGTACCAAAATAATGCACCACAATGATTGCATTCATAGTCAGGGCCACCATAATAGGAGCGATCTGGGTACGTAGCTTTAAGAATTTGCATGTGCTCCTTTGGTATGGAATATGTGAATCTCATCGACAGTGAACGCGGCACATGTTCTTGTCGCAAAATAAGACGCATTTTCCTAGCGGCCTGTCTTTTTTCCCGGTTCACTCGAGCAACACGTGCTGGCACTATTGGGCAAAAATGATCTCTGTTGGGTCGAGAAGACTGAATGTGGCCAGCTCCACAACTCCCTATAGTGCATGATGAACTACCCGTGAGCATTGAGAACCCAGTGGCACCGTGGGATGATGACGGCTCATCTATGGCACATGACACACCACCCGTGAGCTCTAAGTGCTTATTGGCAGCAGATGATATGGAGGACCCATCATGTGGACGCTTCCGCGGGCAGATGCGAACGAATCTGGATGGCTCCATGTCATTTCTTAGCGAGCATTAGCTGACGAAGGCAAAGATGCCCCCCTCCCTCCCCCCAAAAGAAGATGCGATGTGTGGGAGAGACGCCAATTGGAGCCCGCAACCTTAGCGAGAAGTAGCTGAGGGAGGCAAAGATGCCCCCTCCCTCCCCCCAAAGCAAGACGTGATGTGGGAGAGACACCAATCCAAGAGCGCAGCCTCCCCTGGTCCTCATAGGGCTCTCCGCGTAGTGGAGCAGCAGCCGTAGCCAGCCCCGTCGTCGTCGTACGCCCATGGCAGAGCACTATCGTTGCTCCGTCGCTGATGGTCAGATAGGGGATGGAGAAGGGGCACGCGTCGAGAGGATAGCGGCGACCAACGGATGATCCAGCGCACAGGAAAACCAGGACGGAGCAAGG

Coding Potentia
Explanation CPC Score
noncoding -1.01428
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0046100.1 1 36333012 A G
Osa01LNT0046100.1 1 36334877 A T
Osa01LNT0046100.1 1 36326489 A G
Osa01LNT0046100.1 1 36327084 G C
Osa01LNT0046100.1 1 36327112 T C
Osa01LNT0046100.1 1 36327127 A G
Osa01LNT0046100.1 1 36327906 T G
Osa01LNT0046100.1 1 36328447 G A
Osa01LNT0046100.1 1 36329462 A T
Osa01LNT0046100.1 1 36329501 C T
Osa01LNT0046100.1 1 36330401 T C
Osa01LNT0046100.1 1 36332458 T C
Osa01LNT0046100.1 1 36332529 T G
Osa01LNT0046100.1 1 36333006 A G
Osa01LNT0046100.1 1 36333031 T C
Osa01LNT0046100.1 1 36334387 T C
Osa01LNT0046100.1 1 36335611 G A
Osa01LNT0046100.1 1 36336079 A G
Osa01LNT0046100.1 1 36336453 A G
Osa01LNT0046100.1 1 36336508 T C
Osa01LNT0046100.1 1 36335088 T C
Osa01LNT0046100.1 1 36329117 T 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
Osa01LNT0046100.1 osa-miR5528 Translation 5.0 14.338 1 21
Osa01LNT0046100.1 osa-miR5790 Cleavage 5.0 14.542 1 24
Osa01LNT0046100.1 osa-miR5813 Cleavage 4.5 17.593 1 22
Osa01LNT0046100.1 osa-miR1319b Translation 5.0 13.59 1 24
Osa01LNT0046100.1 osa-miR5830 Cleavage 4.5 16.781 1 24
Osa01LNT0046100.1 osa-miR5836 Cleavage 4.0 14.91 1 21
Osa01LNT0046100.1 osa-miR6245 Cleavage 5.0 21.518 1 21
Osa01LNT0046100.1 osa-miR6256 Translation 3.5 20.65 1 22
Osa01LNT0046100.1 osa-miR160c-3p Cleavage 4.5 19.626 1 21
Osa01LNT0046100.1 osa-miR398b Cleavage 4.5 22.17 1 21
Osa01LNT0046100.1 osa-miR159a.1 Cleavage 5.0 13.25 1 21
Osa01LNT0046100.1 osa-miR159b Cleavage 5.0 13.25 1 21
Osa01LNT0046100.1 osa-miR167d-3p Cleavage 4.0 21.547 1 22
Osa01LNT0046100.1 osa-miR169d Translation 4.5 19.391 1 21
Osa01LNT0046100.1 osa-miR169i-5p.2 Cleavage 3.5 21.304 1 22
Osa01LNT0046100.1 osa-miR393b-3p Cleavage 5.0 22.672 1 21
Osa01LNT0046100.1 osa-miR171i-3p Translation 5.0 17.41 1 21
Osa01LNT0046100.1 osa-miR438 Cleavage 4.5 18.242 1 21
Osa01LNT0046100.1 osa-miR820a Translation 4.5 21.035 1 21
Osa01LNT0046100.1 osa-miR820b Translation 4.5 21.035 1 21
Osa01LNT0046100.1 osa-miR820c Translation 4.5 21.035 1 21
Osa01LNT0046100.1 osa-miR444d.3 Cleavage 5.0 15.895 1 21
Osa01LNT0046100.1 osa-miR810b.2 Translation 5.0 15.85 1 21
Osa01LNT0046100.1 osa-miR1435 Translation 3.0 17.047 1 20
Osa01LNT0046100.1 osa-miR1441 Cleavage 4.5 16.47 1 21
Osa01LNT0046100.1 osa-miR1882a Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882b Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882c Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882d Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882e-5p Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882f Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882g Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR1882h Translation 2.0 21.847 1 24
Osa01LNT0046100.1 osa-miR2097-3p Translation 4.5 17.109 1 22
Osa01LNT0046100.1 osa-miR2863a Translation 4.5 17.567 1 21
Osa01LNT0046100.1 osa-miR5147 Translation 5.0 15.008 1 21
Osa01LNT0046100.1 osa-miR5501 Cleavage 4.5 19.816 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0046100.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0046100.1 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0046100.1 1 yd1 Morphological trait Seed C2340 C86
Osa01LNT0046100.1 1 yd1b Morphological trait Seed C547 C2340
Osa01LNT0046100.1 1 qNSB1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0046100.1 1 qSSBp1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0046100.1 1 qChll1a Morphological trait Culm/leaf C86 C813
Osa01LNT0046100.1 1 qH2O21 Others Others C86 C813
Osa01LNT0046100.1 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0046100.1 1 qLVBTS1-1 Morphological trait Panicle/flower C2340 C86
Osa01LNT0046100.1 1 sf1.1 Physiological trait Sterility RM212 RM315
Osa01LNT0046100.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0046100.1 1 nan Resistance or Tolerance Insect resistance RM543 RM472
Osa01LNT0046100.1 1 dth1.1 Physiological trait Flowering RG541 RG109
Osa01LNT0046100.1 1 ng1 Morphological trait Panicle/flower RG374 RG394
Osa01LNT0046100.1 1 sf1 Physiological trait Source activity RG374 RG394
Osa01LNT0046100.1 1 ng1 Morphological trait Seed RG374 RG394
Osa01LNT0046100.1 1 sf1 Morphological trait Seed RG374 RG394
Osa01LNT0046100.1 1 nan Physiological trait Source activity RG374 RG690
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