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

>Osa04LNT0276400.2

ACTCAATCACAGCTTTGATTTACCAGGCCATGTCTCAGATTACAGCTATACAATAGTAACATGCATTCCCAGTCACGTCAATTTTTTTTTCCTTTTAATTGGATGTTTGAAGTTCATTCCTAGCCTCGTATTTTCCACAAAACCACTATTCTATCAAGTGAAAACTCCATACAATGCTCAAACTCTAAAGATCACTATTACTTCAGGAAAGTTCATACAAGGAACTACTGTCTTCAGGTAAGTTCATGCTCTGCGATGGTAGCAGACTAGCAGTGTGTTCCTCCTTTCCGAAATGAAAGGAAACGAGAAGCCTCAGCAGCGTGCTCTAGTGATGCATATTCAGAAACAGACAATTGTACAAACATACCTGTGTCACCGAGGGTGCAAAATGTGAACTGATTGAGCAGACCAAAGGGATGCACCTCTTCTTACTAGCAGTACAATCAAAGGCAGAACATGCTGTCATCAAATTGTTGTAAAAGGCAAGCTAGCCACAGAAGATAAAGGGGATACTTGAGCTTTGGTTAAAAACGATTTCCCATTAGAAATAGAAGCAGCCCATATCTTTGTTGATCATCAAGGAATGATACTCATTGTAGTTAAGATACCCCCAGAAACGATAAAGACCAATCTCCCCATATTTCGAAGACTTCAAATGCAAAATATACAAATCTTTGATATTACCCTCAAACTTCGTTCTAATAGCGTCCACCTGAGAGAAATTTATAAGAGAATCCAGATTAAGTTGTTTTACTGTTGACTCAGAAATGTAATTGAGGCTCTTAAAACATGACCGCAACTCCAAAGCTTGTTGTAGAATGCTATTAATTATGGCAGCAATTGGTTTTGTTTCAGCAGATAAGAAACATATGTGAAGCGCATCAGTAACATAACATAGATGCACATACTCGAGATCCAGCATATCTCTCACCTGATGTTGAAGTGAATGTTGAAAACGGCGCCATGATATATCAGACAAATGGCAATGGAGATACTGTTGTAGTGTTGATAGAAAGTGATAAACTTGATGTCTCAGTTTCATCACAGAACTCAATTCCTTTAAAACATCAGGTCTATTATGGCTGGAACGACTGATTAACTGTGTTAACTCCTTCAGAAATCGCCACACTTCAGTCAGAGAAAACACTGCAAGCCTAACCTGAACAAGATACCGAAATATTTCAGCATATGTTTTAAGTGCCTCCTCTGTAATGACGATGTTCACTGGCCAATCAACTTTATAGCCCAATAAGATGTCGTCCAGCACATCAAGACCACATGTAGAGGCTTTAAGAGAAACAACTGGTTGCTCATTCATATATACAAACAACCTTTCCTTATAAGGGTCAGAATCGCATGAAGACCTCTGCAAAGCCAAGTCAAGAAGCCCTTGGATCTCTGCTCTTTTGTGCTCAGACTTGACAAAGGACCACTTCTTTTTATAAATAGAAACAATAAAAGAATCTGCCCAATCAGCCAGTTCCATAAAATGGTAACGCCGCAGTGCTTGTAAGTGTCCACAAAGATCAAAACCATCCTCAAGCAACTTCATCGTGAAGCTGCTTACATATTTATATTGCAGCAAAACTTCTTGTATAATGCACTTGTCAATAGCTATATCAAGTGGCATATCAGATGATGAAGTGGTATCTCCAGCTATTTCCATTGATTTAGCAGTGTACTCTAATGATTTCTCCCAGAATGCCCCACCCGAAGGATTTTCTAGAAGATTTGTTTGTGCTGAGATGTCTCCTGGGGAAGTAAGATAAGCATGACTTGTTGTCTTCGATTGAAGAAGCTTGCTGGAACAATCAAACTGTTTAGAAGCCTGAGCATTGGACTGTACAGCCATTGCAGATCTGACTTCAAACTCATCAAGGGAAGAAGTACTTCTCCCACAATATGCTTCACATGGATTAGTTACTGACTCAAAATTAAAGCCAATAAGTGCTTGGTTCTTCCTATTTCCATGCAAGTCATGCTCCGTATGACAAGAAACCGCATTCTTCACTATTGGATTAATGCTAAAATTGTAAGGAATGTTAGTATTCCATGGTTGCTTTATATTGATAGATTTTTCATCGTTATCCCTATTTGGCAGTCTAGGAGACCCTGATTCAGAGTGTCGACAAACAACATTGGCATGTGATACTTGCTCTGCACCTTTATCTCCTGTATATAAGAACTCTTCAGCCAAACTCATTTTTCCAGAGGATATATCGAATGAATTCTTCAAGAAACTGTCGAATGGCCAAAATTCACTGTATTGATTGTCCAGTTCCAAAGCATCACAGACCACGTCATGTTCTATACTCTGCGAGTGCATAGGAACATGTCCATAACTCAAGTCGTCCTTTTTCTTGTTCTCATTGATAGGGCTAGCAGGATTAATCCCATCAGAAACAGAACAGGTTTCATATGAAAGTAACTTTGTGGTTACAGATGAGCATTTTGCTTCACCTGAACTTGCACGGTACGATGAGAACATCGAGCTAGGCATATTATCACAAGCAGTATCAATCTCATCTTCAATATCATCAATAGAACTATATGATGAAGATGATTCCGATGATTCTAATGCATCCACTTTATCTGAAGATTCTTGTGATGTTGAAGAAGCATCATTATCTTTAAGCTCTGCAACCACATTGCAAGCTGGTAGAGCATTTGTGCCATGATAGAACAGCTCCACATCTGAAACAGCTGTATCTAGAGGGCTTGTACTTATATGCAGAACATTCAGTGCCGCATCAAAAGGAATTACCTCAACATTTGAGAAAAAGTGATGGAGCTTCTCTATCATTGACTTGTACATAGCATCTCTTTGACATATTACTGCTTCCACCCTACTTTTTGAGAAAGTGAATGAATTCATTGAAGACTCGATGGACGTATCAAACCATGGGAGAATTTCCTCCAGATGAATGATGTGACGAGATGCATGAGCATCTCCTCCAGTGTCAGAAAGATTACACGATTCTAGAAGCTTCATGAGCACTTGAAGTTGTTGTCCAGTGCGCAGAAGAGGACCACATACATCTTTTAGAAAGCATGGTGCAGATACATGATTTGCTCCCTTTAAGGACAACAGGGTGAAATTATCTACTGGGTCTGAAGAACCTCCTTGAGTTCGCTTATTCTTAGCTTGAGTTATGAGAAATTCCTCATAAGGATCATCAACAGAAGCTCGGTAAATCCAGGACTTGATGAAATTACAATATGGCTCACAAGAACGAACAAAAAGATATTTTAGAAGTCCATAGTGAACGGAATCGGCATCAAATAGGAAAGCAAATCAGTGCTCCATGGGAAGTTCTCAAACCCCAAGTTAGAATCAGTTGTCAAACCCTCCTGGCACAACGAAAGACCTGCAAACTTCGGAAAGCATATATTTCCGAGGGACTTAATATGTCTTCTTAACTCCTCAGTGTGGAGATAAACTTCCAGAAGAGTGATTTCAGAATTAGAATTATAACTAGCTCCATCTGGGGTCATGGAAGGTATATCAGGTTGTCCCTCCAAACGCCTCAGCTTAATTGATGCTGGTAGAGTATTCAAGGAACAAAAATAACCTTCTAAAACCTTTTCAACTGCTGCAGCAAATGCTTGGTTCACTAAACTGTAAGGAGCAGGTTGTTCAGTTTCTTCGCTATCAGAAACTTCATGTTCATGTCCTTCTCTACCTCGACCATTCAATTCTCGACTTTGGAAAAGATAAAAATGCAGAAACTTGCACAGGAAGAGAACTGAAAGACCTGTAGTGCGTATAGATTTGAGAATATTCCCTACAGAGGTAGTACTGGATGAACGTGACCACACGTTTGCAACACGATGAGAAGTCCTATCAGCCGGACATGAGAAGAACAGCACAGAGAGCTCCTCAATCTCATCTAATGATGATTTGACACCATGCAGTGCATGCAAAGCCAAACGAACCAAAGAAGCATCCGGAACCGATGCGAGCTCGTAGATCGGATCCCCCCGGAGCCGCCCTCCAGGGTTGGCGGTACGGGCGGCACCGCCAGCCTGGGTGACGGACTCCCAGGTTGCCGGCGGCGTCCACGGGCCGACCACTCGGAGGGTGGCGAGCAGCGACGAGAGGCTGGAGGCCGCGGCCTCCATCCGGGGAACGGTAGTCAGCTAGGGTTTAGACCTCCAATGTCAGGCCTTATTCCGAACGCAATGAGAGGAGGAGCGGTGTTGTGCTGGTTGCAGCGAGCGGCAGTGAGGTACGGATCGCCGGAGACGTGGTGGCTGGCTGGCTGGCTCCGGCGAGAGGGTGGGAGTGGGAGGGAGGTCGCCGTCGCCGTCACCGTCACCTGCCCGCGGTTTCGGAGAGAGCCGGCGGGAATTGAGCCGCGAGGGGAGCAGTCCGCAGGTGAGAGGGTGAGA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.815564
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0276400.2 4 28486682 T C
Osa04LNT0276400.2 4 28486435 T C
Osa04LNT0276400.2 4 28486916 A G
Osa04LNT0276400.2 4 28487544 T C
Osa04LNT0276400.2 4 28486672 T C
Osa04LNT0276400.2 4 28484198 C T
Osa04LNT0276400.2 4 28486636 A G
Osa04LNT0276400.2 4 28486797 A G
Osa04LNT0276400.2 4 28487107 G C
Osa04LNT0276400.2 4 28488200 A T
Osa04LNT0276400.2 4 28488741 G C
Osa04LNT0276400.2 4 28490303 G A
Osa04LNT0276400.2 4 28491650 T A
Osa04LNT0276400.2 4 28491705 A T
Osa04LNT0276400.2 4 28492160 G A
Osa04LNT0276400.2 4 28492179 A C
Osa04LNT0276400.2 4 28492444 G C
Osa04LNT0276400.2 4 28494128 T G
Osa04LNT0276400.2 4 28494263 A C
Osa04LNT0276400.2 4 28487668 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0276400.2 osa-miR5537 Translation 4.5 16.649 1 22
Osa04LNT0276400.2 osa-miR5804 Translation 4.5 15.137 1 21
Osa04LNT0276400.2 osa-miR5817 Translation 4.0 7.942 1 24
Osa04LNT0276400.2 osa-miR1861o Translation 4.0 12.904 1 22
Osa04LNT0276400.2 osa-miR395c Cleavage 4.0 20.442 1 21
Osa04LNT0276400.2 osa-miR395u Cleavage 5.0 20.442 1 21
Osa04LNT0276400.2 osa-miR395u Translation 4.5 16.437 1 21
Osa04LNT0276400.2 osa-miR396a-5p Translation 4.5 13.628 1 21
Osa04LNT0276400.2 osa-miR396a-3p Cleavage 4.5 13.941 1 20
Osa04LNT0276400.2 osa-miR396b-5p Translation 4.5 13.628 1 21
Osa04LNT0276400.2 osa-miR396b-3p Cleavage 4.5 13.941 1 20
Osa04LNT0276400.2 osa-miR396c-3p Cleavage 4.5 13.941 1 21
Osa04LNT0276400.2 osa-miR167d-3p Cleavage 5.0 21.394 1 22
Osa04LNT0276400.2 osa-miR167h-3p Translation 4.0 13.532 1 21
Osa04LNT0276400.2 osa-miR393b-3p Translation 4.0 14.552 1 21
Osa04LNT0276400.2 osa-miR417 Cleavage 5.0 12.593 1 21
Osa04LNT0276400.2 osa-miR426 Cleavage 3.0 20.105 1 21
Osa04LNT0276400.2 osa-miR426 Translation 5.0 10.647 1 21
Osa04LNT0276400.2 osa-miR535-5p Cleavage 4.0 14.472 1 21
Osa04LNT0276400.2 osa-miR395o Cleavage 4.0 20.442 1 21
Osa04LNT0276400.2 osa-miR810a Translation 5.0 22.594 1 21
Osa04LNT0276400.2 osa-miR815a Cleavage 4.5 7.817 1 21
Osa04LNT0276400.2 osa-miR815b Cleavage 4.5 7.817 1 21
Osa04LNT0276400.2 osa-miR815c Cleavage 4.5 7.817 1 21
Osa04LNT0276400.2 osa-miR1438 Cleavage 5.0 21.144 1 22
Osa04LNT0276400.2 osa-miR1861a Translation 4.0 12.904 1 22
Osa04LNT0276400.2 osa-miR1861b Translation 5.0 12.904 1 22
Osa04LNT0276400.2 osa-miR1861d Translation 4.5 12.904 1 22
Osa04LNT0276400.2 osa-miR1861f Translation 5.0 12.904 1 22
Osa04LNT0276400.2 osa-miR1861i Translation 5.0 12.904 1 22
Osa04LNT0276400.2 osa-miR1861l Translation 5.0 12.904 1 22
Osa04LNT0276400.2 osa-miR1878 Cleavage 4.0 10.299 1 24
Osa04LNT0276400.2 osa-miR2090 Cleavage 5.0 15.731 1 22
Osa04LNT0276400.2 osa-miR2101-3p Translation 5.0 12.117 1 22
Osa04LNT0276400.2 osa-miR2122 Cleavage 4.0 12.469 1 22
Osa04LNT0276400.2 osa-miR2922 Translation 5.0 17.756 1 20
Osa04LNT0276400.2 osa-miR5484 Translation 5.0 18.197 1 21
Osa04LNT0276400.2 osa-miR5538 Translation 5.0 13.185 1 22
Osa04LNT0276400.2 osa-miR2905 Cleavage 4.5 20.919 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0276400.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0276400.2 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
Osa04LNT0276400.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0276400.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0276400.2 4 nan Morphological trait Root RM3288 RM5503
Osa04LNT0276400.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
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