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

>Osa04LNT0275500.1

ACATAAAATCTTTGACCAATTAACGGCGAATAGTCTCAGCATAACCTCTATGTGATGGTTGCATCCGTATACTCAAAACATAGCCAAATGCCAAAATTTACATGTACAAAAATGGGGTTGCTCACACTGGTTCACCCTACAGAGAATTGTAAGACAGAAAACTGTCTGAACCGAGCAACCAAAAATGGATACAACGCTGCAAACAATGTAAAATGACTATTCACCCATTCTACAAAAAGAAAAACCATCGGGATTTTTACAGGGCTACTCGATAAAGTTCGTTTACTCAGCAGTTCGCTGAATAATATGATCTGCTGGATATGGTGTACGACCTAGCCTTTGCTCAGCCTAACTCGCAGGTCCTATTACTTATCCACTTTGTACAGATAGTACATCTCGAGCCATCGATTCATTATGCTAACACGAACAGAAAATGATCTTTAAGCTAGTAATGATTTACCAAAATAAATGCTTTTTGCTCATGACTGAAGAAGCCCGTCACCTTCCCAACCAAGACGTAACATCTGATCCACTACCTTCAAGCTCAAAGCAGGATCAGTGAACACTATTAGCTGCTTATCAGCAGTAGACAGTAGAAGATTTGTGTTCTCTTTGTTTAGAGCGATTGCTGTGACGTCCTGGCCTTTCCCCAGCTCCATTGTATGAAATACCTTAAGTTTATGCAGATCAACAAAGCATACAGAAGGCACATGAACAGATTGCCTAGTTTCAGCTTGTTTAGATATGCCATCCTTGCCATTTGGTTCATTAGGTTCATGATCCCCAGTCTCAGTACTGTCCTCACACTTATAATTGCTTGAAGAACATGTTCCCATTAAGGCGAAATGGCCATCAGTAGAAATCTCAATGCAACTAACCCGTCCACAAAAAGGTGATAGAACTGTGGTAGCAATAGGGAGTCCATTGACAGTGAATGTAGATAGTCTTTTCTTTGATTCATTCCAAACCAGAATGACCCCTTGAGAAGATAAGCATACAGCATGTGCCTCCGCTACATTAAGCTTCCTTATCAGACGACCAGTCCTCAAAGAATGTAGAAGAACACCTGACATGTTTGATGAGGATACAACAAGTCCCAAGTCAGGACTGACTGAACAGCTAGTCACTTCCTCAAGATGTCCTCTCAATACATGCATAGGACCTTCAATTCGACGCCTCCTGATTTCTGTAAGGTTGCTCACACTAGGACTGCGTGGTGTTGTCGGAGTTGTTGGTGGAGGCTCAGGGGCATTTTTCTTATGTAAGGAGCCTGCCTGATGAATCCTCCAGAGTATAACTGTGGTATCTCGAGACCCTGTTACAAGGTAGTTGCTATCATGAGAAAGTGCAAGGCAGGTAACAGGAGCAAGATGTCCAGTAGCAGTTTCAATAGTCTTCGCTCCATCTGGGGAGATCAACTTCACAGAACCATCAGCATGCCCACCAGTGATAATCTCTTTGTCACATGTGACAGCAACAACTGCTGAACTACGGATGCCAGAAGCAGCAAATGCTATAGCTCTTGGGAAGTCATAATCTTCTCCAGAACTAGCAGATCCTTTAAAAATGCGCATCAGTGCACCACCGGTTGAATTTGCAGCATTTCTACCATGATGAAATAGAAAGGGTGTCCCTTGGCCATCTGGAGTATTTGGTTGCCAATGGTGAAGTGCCACATGAGCAGCAGGCACATTTACATCTACAACTACAATAGAGTCATTGGATACAAACATGGTACTGGCCGGAACATTGCAGCGATCTGGATTTGGAAGTAAATATGATTTAAGTTCACTTGGATTCCGGAATATAGTCTGTAGATGTAAAACTTCTGCCAATGGCTTTCTCCTCATGTGGGGAATAGTTAGCAATTGAGATGGTGTTTGTCCAAAGTAAGCAATTTGATCTTGCATGGCTTGCCGTTGCACTGGATCTGTGATTTTGTCAATGTCCACAGTTCCTTCATATGTAATGTAGAAGAACACATTGTTGGCCATTACTGCTTCTTTACCCCTCTGTTTAAATCCAAATATTAAATCAATCCACTCATGCAAATGAGCAGAAACATGCTCACTCTCAAGAGCCTTCCGGTGTTTATGGACAAAATCAACAGGGTCCTCAGCCCAAGGAGGCAAATTTACAGAATCTAGCTTTCCTCCAAGCTGAGTTGTCCCGAAGTCGATAGAATTTATATTGGTAAATACTTCAGGGAGGTAAAACATCTCAGGGACTAGCTCTTTTACATCACTCATGTCTTCAAGAACACTGTCCCATGTACCAGATAGATCAGAAAACATACGATCAGCATGATCAAATTTGCCGCCTTGCAGCTGTATTGAGAGCGTAGTATAAGGTTCCACCCTGAAAAGGTAATACAAGACCGTGCCAGCACTGGAGTAATGTGAACCATAATGGAACTTTGGGATGATTGGATCCTCAAACGTAGAGTAGCGCTCTTGGAATTTTTCTAGTCGCTCAGGGTTTAGTGCACCAATCGGCTTTGAAAGATCCCGATATGTACATGGGTCATCCAGATTAAGAATTTCGGATCGGTAATCAGCAATTATCCAAGGAAAAACAGGATACTGAGTTATGTCATTGTAACTTCGTCCAGCCAGTGTGTTCAGTTCCATCAAGTACTCAAAATTGCTAATCTCCCAGTTAGCCCAGCGCTCCGTCAACTGAGTTCTTTTGAGAATTTGCTCAGCTCTCTGGGTAGCTAGAAAAATGTCATTCAAATTGGGAGGCTTGCTGTGAACAATTGCCCGATAAGCATTTTTGCGTGCTTCCATATCCCCAAAATCAAAAAAGAAATTTGACCTATCTACCATAAACAATTCCAAAGCACTTCGCCGCAACAAATATCGTCTGCTATATATCTGATGCAGAGAGGAGATCAACCAACTCCTATCTTTATCCTGTTGATCACATTGGCCGCTAGTGGACGCATGATCATCCATGTTACTCTCGCTTGCACTCTCATCAATTATAAAGTTAATCCTCTTAGATGTTACTTGGAATGTTCCTCGTACAACTTTCAATGGTCGCACCATCGACGATGGAAGCTCAACAATAATTCTCTCATCAGCATCACTAGGCACATATCCAGGTGCAATAACCGTCGACCGAACCAAATTGCGATCAGCAGAAATGCCAGAACCTCGTGAATCTATTGATCCTTTCACAGACTGTTGATCTGCTTGTTGGAGTCGATCGTCAACACTGCTTTGAGTTGTGTCTGATTCTAACTGCTCATTGTCCTCATTTCTGTCATCCACTGACATGGCCTCAGCCGTTATTATAGGTGCAGTTGATGGAAGTGTGTCTGTTACTAAAGGTTCTGTACCCTCTGGGTTGCATTCATTTGATTGTGCAACATTACTTAGCTTTCGCTCTTCATAATCAGCAGCTGCACCCAAATGATCAGACCCCTTGTGGTTCCTTTTCATAAATCTTCTCATCCTTGAAGAACTTTCAGTAAAATCTAATTTCCAGAAAATACGATCAGGAGCACACAAGGGTTCACCGAAAGGTCCATATAGTCTGTCCATCTCTGTTAGGCAATGAAGAAGATGGCGCCATGCTCGAACTCCAGTTGACACCCGATGTCGATTCAGCACATCAGCTTGTGTTTGCCTCTCCATCTCAACTCGCTGTAAGTTCCGCGCCAACGCAAAACCAGAGACAAGAATAGCGACATATTTGTATGAAAGGGCTGAAAAATCCCTTCCTGAAACTGACTTGGAATCAACTGATTGCAGGCACTCCATCCAAGCAGCACTCATAGCTTCAGATGTGTTCCACCTCTTTGCACGCTCAATATCACCTGCACTCCTCCTTTGTCCTGATGTTGCCATTGCTACAGCACTAAGACCCCTTCCTGAACCAATCTTAGCAGTCCGCTCAAGGTCCCGAGTAGCAGCTAATGCTGCTGCTTTGACAGCTGCTTTATCCTTTGGTGTGGATCCATGCTTGTTGGGTGCTGTTTCAATAGGCTTCTGGAAACTTGTAAAAGACTGTAGTTTTGGTGCTGCTTTACGCTCAGGCACTGACGTGTCACGCCTGTTCAAGGTCCTTGGAGGTGCTATTGCTTCTGTTCCAGAGGCACCAGCAGCCATCATGGCTAATGCCAATGCAACAGGTGGTGAGGCAAAAGCAGCAGCCCAACCAGGTGATATCATTGAAAGAGCAGCCTCAATGGGTAATGCATCTGCTGCCAAAGCGCGATCATCAGCAATCAGTGGATTTTGCCCATCTGAAGAAGTTAGCTCATGAATACCAGCCAATAGTGGACGCCACCTTCTCAAGATGGCTATAAATGGTGGTAAAATCAGCTCAATGTACTGTTTCCTTAGGGGGCTCCTGTCCCTACCAATAGCATGCCATACCTCTGAATAGAGAATAGAGGAAGCAACCAACACCCTTTGTCTCTTAGATTCATTAATTGGCATATTGAGAATGGGACCAAGCACACTCCACAGAAGTGCAGATCGGGGTTTCCTTGTAGATGAGCGATTGTTGCTGTCAAGTGGCATCATGCTTCCAGCTTGATGGCCCAACCCTTCCGATATGACATCTTTTATGCTGATGTTGCCTGTGAAGGCATCACCTTCACCATTGTCATCCTCCCTCATTGAAACAAGAGTCATTCTGAGCATGCAAAGGAATGGCTGGTCGCTATCCAGCAACTGATAAAGTGCAGTCATAACTCCCATACCAGGGCCGGAGCCCCCTCCAATACCTAGACCACCACCAAGTCCAGAATCATCTAACAGCAATGCCTGCAGCACTGCAACTGATTTCTTCACAAGTGGAAGGTCAACCCAAGTCCCATTTGAGTCCTTCTCCAGAACAGATTTCCAAAATTCCCAACCACTTCCACCGCCACCAAATGTATCAGATTTGGATGGGATTCCAACGCCATACCACAAGCGGCTCCTGTACTTCCAACTTTCAGCAAGATCTGCAATGCAGCTCCCATAAGAAACAAATGCATGTTTGACAGATTCATAAGGTTCAGCTGCTGCTGCTGATGTAAGACGCTCCATCACAGCAGCAGAGATTTGTCCGTTTGAATCAGCCATTGAAGTAAGCACATCTAATGGAAGGCCACCAGCATCAGTGGACAAAGATGATCGTCTTGAGGTCCCAGCATCCATAGGCTCATTACCACTTCTACACAATGAATTTGATCGACTGGCAGCAGACGAAACCATTGAGGCAGAAGGGACAGCACTATCAAGTGATCTGGATGTGCAAAAATGTTGACCTTGTGACCTCAGATGATCTTCTACAAGCATCAGAATAACTATTGCATTTTCCGCTAGTGCTACTGAAAGATGAGCAGCATTTTCCGCTTGGGTTTTTGCTTCTTCAGGAGATAAACCCTCAGCTGCAACACCAGCTGCAGCTGCAGCAATTACTTCAGTCTGGACTTGAAGTTCTCTGGCAGAAAAATCAAGCAGACCGCCTAGCAATCTCCTTTTTAAAATTGGCAATGATTCTTCCCGTCTGATTCTTTGGTCTCCTGTGCTAGATCCTCCAACCATTGAAAGCCACTCTGCACAATGAATTGTTGCTTCCACATCCTTCCACCCATCTTTTTGCCGCATTGAATGCTCCAACATGATAATCAGGAAATTGTGTATGAGGTCTTCAATATCACCAATGCTTATGCCATCAGCATATTTCTTAGCACCCATCTCATGATTATAAATCAAAACCTCCAAAATCCATTCTGGCCATTCTGAAATTGAGGTCATCGTGGTTCTATTCTCTGGATGACTGCAAGCCAAAAACAGAAGATCCTGTATAGCACGAGATTGGAATGACCTTGATGCATATGGAAGCGAACGGAGCAAGACTAGCAACAGTTGAATATGTTCAAAACGGTGGCCACAATCATATAGGTTTAGATTTTCATCAACTGAAGAAACATTGATCGCAGCAGAAATTAAAGCCATATAGACATTTACAGTCATAAGCCTCCTTGGGGCTGCTTGAAATGCTTTCTGCAGAGCAAACAGTAACAGTGACACTCTATCTTCTGACATGGTATTTCCTTCTTCATGAACTGTCGTCAGAAGGCCACCAGGTAAATTTGGATTTGCAGCCCTTGAGGCAAACTTTAGGTGACCTGATGCAACTAGAGCACCCAAAATGTGAATGATTCCAACAACAATGCCATCACCTTTGTCAACATTGTAAACATTATTCCGGACATTGTCAGCAGTAATTGAGAAGTTGATGCCACCCAAATTCTTTAGCAGCTGATTTTCAGAACTGGACAACTTCCTTCCTATACTTGATCCCAAAATCTCACAAGGCACATCATTTGTGCTTGTAGATCCCAGCTCAGTATGTTCTTCATGAAGGATGGATTCGTGCTGTTCAAGTTCAACTGATTGAATTTGATCATCCTGGCTCTTTGCTTCACCACTAGCAGCTTTTGTGTCTGAATCATCATTCCTTAAAAAATCATTTTCACTTAAAAGTGCATCAGAATTGTCCAAAATACTGTTGTTACCAGCTTTAGCTTCCCTCTGTAAAAGAACGAGAAGTGCATCCACACCACCACAAGATATGAATGACTGAGCAAACATGTTGGCTCTAGAAATGTTAGGCTGCACAATCAACCTATAGATGAGGTGCAACACCCTTGCAACCTGATTAGGCTGTGGGCAATCAACAACAAATCCAATCAAGCAGCGAACATCATCAGAAGCTGCTGTGGAAGATGCTGATCCTAACAGAAGTTCAACAACAACCAAGAGTTCATCAATCAGAGCATTAATTTCACCCAAGGATCTCTTTGTTCCAGTAAGGGCAAAGTTATCGATCGAATTTGGTTCCCGGATTGCCCAGTAGCACCTTCTGCAGCTATCAAGAAGCATTTGCAATGCATTTGCATCCCTCATGCAAGCAGCCTCTGTAAATATCATGTCTGCAAGCGAGGACAGAAGCTTCTTCTGTAAACCATAAGTACATGAACTCCACATCTTCAGGTCCAACAGCAAAGTACTGAAAAGCTGCACTTTAAGCTCATGGTTGTTTCTTTGAGATTGGCACAAGGATACAATTGCATCAACTAGCTCCTCATCAGTCACTGCCTCCCCCTCTCCACCTTCCATCTTTGGAAATGCTTGTAATTGGTAATGTAAAACACGTGACAAAATCTCCGGTGAACATGTCCGACATAATTCTTCATTATTTCCAGGATGCTGAATAGCCAGGGAAATAATCCTGAAAATTGGGGCAGAAAGAGAAGCAGTGGCAATCGACAATTCACCAAGCATAGGTTCAAGACTATCCATCTGCACATTGCTTATAGTCAACGGAAGTAAAGCCATTGGACCCCCATAGGCTAAGGCCCATAAAGACTCCGCAGGCCGCACACGAGATGAAACATGAACCAACCCAAGAACTTCTGCAGGCCTTCGGTGAGTGCCTGCTGAGCCAGAAGGGGAAGCATCTGGACATAATCGTCCATTCAGAAGACTAGGATGATAAAGAAGATGTAAGCATCCTCCTATCTGTTGGTTCAATGTAAAACTCTCTTCGGCCATGTTCTTAACATGGTCATTGGTTGCTCTCCAAGGCAAACCTGCACCATTTCCAAAACTAGGGAGTACATCTCCTCCACGGGATGCCAGACGACCCATCCTTTCTGGCCCAATTGGCTCCCTAAAAATGTATATAGGTCCCATTTCTGCAAACAATGGACATTGTCGCCTCCGCCTCTGCAGGCCTGCAATAGTTGGTGGAGGATTCGTTCCAATGCAGCAAAATGCTAGTGGTTTTGAGATGCGTGGGAACTCAAAAGGACGACTCTCATGCAAGCTTCCATCAACGTACAACCGCAATTCACTGTCGCCCTTTCCAAGCAAACCATGCTTGTTTGTGTGCTCCAACCCAACGAAGTACCATCGCTGAGGTTTAAACGCATAAGTGAAGTGCAGAGAAGCCTTCTTACCCCTCCCACCCCCACTTTCCACCACCAAGAACTGTCCATGGAAGTAAGCCTCCACACCCTGATTATCTGAAGAGAGAAAGCTAAAAAGTCTAGGCATGTGTGTTGTTCCTTCTCCTGCAAGAGCGCTGGCTGCAGCAGCTGCTGACATTGCTGATGATTTTCCAGATGTTGCTGCGGCTGCAGCAGCAATGGCAGCTGCAGCTGTTGCTGTACTAAGTGTATCTGAGAATGATTCTATGTAAATCCAAGTAGCAAACCCGTAGCCATTAGAGAAGGGCCACCTGCTGTCACCAGGGCCAAGCAAGCCAGAGCTCTCCCCGTCAAACTCAAATGTCGCAGCAGGACCTCTTGCTTCCTCACTCCCCATGGCTTTCTCAAGTGCCAGCATCAGTGGTGTTGCCCAGCTTGTACCAAGCGCCTTCTTAACCAAACCAAGCCACGAATGCAAGTCCTTCACGCTAAGCGAGTGCCCACCCAATAGCTGGATGCAATGGAGCAGTGGTGTTCCGTCCCAGCTACTTGCCCGACCCATTCCAATGAGTAGCTTCTCAGCAGAATCGAGGAGGACGGGTAGAAGGCCCGATGAAGAGCACATGGCACGATTGCGTGTGCAGGCGCGGAGCGTGGCGTGAATGCCCACGGCCATACGAGTGCGCGGAGATGGCTCATCGCCGCAGGGGAGGTAAGGCAGGAGCTCCGCGGCAACAACGGCGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.36564
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0275500.1 4 27800401 G A
Osa04LNT0275500.1 4 27796419 A G
Osa04LNT0275500.1 4 27796616 T C
Osa04LNT0275500.1 4 27797909 G C
Osa04LNT0275500.1 4 27798829 A G
Osa04LNT0275500.1 4 27799599 C T
Osa04LNT0275500.1 4 27801414 A G
Osa04LNT0275500.1 4 27801733 C T
Osa04LNT0275500.1 4 27802295 T C
Osa04LNT0275500.1 4 27802607 C G
Osa04LNT0275500.1 4 27802960 C T
Osa04LNT0275500.1 4 27805091 G A
Osa04LNT0275500.1 4 27806652 C T
Osa04LNT0275500.1 4 27807415 C A
Osa04LNT0275500.1 4 27807519 G A
Osa04LNT0275500.1 4 27809659 T A
Osa04LNT0275500.1 4 27809660 A T
Osa04LNT0275500.1 4 27810174 C T
Osa04LNT0275500.1 4 27810220 A G
Osa04LNT0275500.1 4 27811739 G A
Osa04LNT0275500.1 4 27812423 A G
Osa04LNT0275500.1 4 27812497 A G
Osa04LNT0275500.1 4 27814313 T C
Osa04LNT0275500.1 4 27809817 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0275500.1 osa-miR5529 Cleavage 4.5 20.261 1 21
Osa04LNT0275500.1 osa-miR5538 Translation 4.5 17.787 1 22
Osa04LNT0275500.1 osa-miR5542 Cleavage 4.0 14.277 1 21
Osa04LNT0275500.1 osa-miR5542 Translation 4.5 22.364 1 21
Osa04LNT0275500.1 osa-miR5791 Cleavage 5.0 12.407 1 21
Osa04LNT0275500.1 osa-miR1319b Translation 5.0 10.839 1 24
Osa04LNT0275500.1 osa-miR5833 Translation 4.5 24.044 1 21
Osa04LNT0275500.1 osa-miR5835 Translation 4.5 22.575 1 24
Osa04LNT0275500.1 osa-miR5837.2 Translation 3.5 9.956 1 21
Osa04LNT0275500.1 osa-miR6253 Cleavage 3.0 18.319 1 22
Osa04LNT0275500.1 osa-miR6255 Cleavage 5.0 18.837 1 22
Osa04LNT0275500.1 osa-miR7695-5p Cleavage 4.0 20.1 1 24
Osa04LNT0275500.1 osa-miR167b Translation 4.5 21.563 1 21
Osa04LNT0275500.1 osa-miR396a-3p Translation 5.0 17.984 1 20
Osa04LNT0275500.1 osa-miR396b-3p Translation 5.0 17.984 1 20
Osa04LNT0275500.1 osa-miR397a Cleavage 4.5 16.647 1 21
Osa04LNT0275500.1 osa-miR171f-5p Cleavage 4.5 15.726 1 21
Osa04LNT0275500.1 osa-miR419 Cleavage 4.5 16.829 1 21
Osa04LNT0275500.1 osa-miR426 Cleavage 4.0 10.456 1 21
Osa04LNT0275500.1 osa-miR438 Translation 5.0 21.286 1 21
Osa04LNT0275500.1 osa-miR530-3p Cleavage 3.5 17.813 1 21
Osa04LNT0275500.1 osa-miR1423-3p Cleavage 5.0 22.029 1 21
Osa04LNT0275500.1 osa-miR1853-5p Translation 4.5 15.558 1 24
Osa04LNT0275500.1 osa-miR1860-3p Translation 4.0 20.357 1 22
Osa04LNT0275500.1 osa-miR1873 Cleavage 5.0 16.046 1 24
Osa04LNT0275500.1 osa-miR1862e Cleavage 5.0 18.405 1 24
Osa04LNT0275500.1 osa-miR1320-3p Cleavage 5.0 17.794 1 21
Osa04LNT0275500.1 osa-miR2092-5p Translation 4.5 18.576 1 21
Osa04LNT0275500.1 osa-miR2095-3p Translation 4.5 17.798 1 20
Osa04LNT0275500.1 osa-miR395x Cleavage 5.0 6.82 1 21
Osa04LNT0275500.1 osa-miR395x Translation 5.0 23.691 1 21
Osa04LNT0275500.1 osa-miR167a-5p Translation 4.5 21.563 1 21
Osa04LNT0275500.1 osa-miR167c-5p Translation 4.5 21.563 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0275500.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0275500.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0275500.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0275500.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0275500.1 4 qCTS4-3 Resistance or Tolerance Cold tolerance RM241 RM317
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