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

>Osa02LNT0179500.2

TCGCTTTACTTCTTCTCTCTCTTTTCTCCACATGTGCTTACAGGTGACTTGTAGCCTGTTATTGTACTCGTTCTTACTCCACATGTGCGTGCTTACAGCTAACTTGTAGCCCGTTATTGTACTCGCTCTTACTGATACACTCCAGTTCACCCCACCCAGTTGCCCACAATACAAAAGAACACCGATGCACAAAATCCATAACACGACTCACCAAAACATTTTATACAGCGCGTAGCATGCATGTACAGATGTACCTATATGTGGTCTTACCTCTCTTGGATACCATGGAGTCAAGACTTCAGGATTACACAAACAAAATAATTTTTCCTCCAGTGAAATTAGAATATCGAATTTCACGAGGGATTTAACCGCGAATGTCATTTCTAAACTCCTGATTTTGATGACCAAGTGGGGACAACCACCACGAAGGTAAACATCTGAAAAAAATTCAGTGCCAAACAGGCAACTGGTAGCCAAAAAGGCTGGATTGAACGGGCCAATGAGCAACACACGAGAAATAATGATTTGGGTGGTGCCGAGGGCCTTCCTCTTTTCCCTTCTCTGTTGGCATATGTATAGAAAGTACCCAATGCCTCCATTAGTGCTAACCAAACCCTCCAAGCTTGTAAGGTCATTGTGACCACATCAAGCAAATAGCTTCGCTCCCACCAATCGCCATCAAGCTTGCATCAATTCTGTGTGGCGAGCGACTCAATCTGTGTATCCTTGGGCTCCTACCGTTGACAATCTAATGTCCTCTTTAAAAGAAAGGGCATGACATCCAGAGCAATATGTTCATTTGTTCTCATCCGATGTCTGTGAAATCTGTAAGAGGATCCAACTCCTCAATGCCAGAAAGGACATCAGAGTCATACTGGTACGGAACAAACTCTGTTTCAGCCTCTTGAGGAAGATTATCAAAGTAGGTGAATTCAGAATCACTGATGCCAAGGTCAGATAGGGACTGGGTAATGTGGAACTCTGCTGAGTTATGCAGAAGTTGCCCCGGAATCCTATGAAAATTATTTGTAACCGGCACTTCCTGTGGTTCAGTGGTCCTTTGAATTTTGGATTTGGGAGGCCTTCCAGATTCTGATGATGCTTTGTGCTTTCCTATGGACTTAGGACCAGATTTATGCCGACCGGCATCGTATGTGTGGAAAGCAGATGAGGCCCAGTGAGAACCTTCCCCTTCAAAACAAGTTTCTGATACCATCCTGAATCTGTTCTCAGCATGTCTATAAGAAAGTGTGGACAGTAGTGAGTGCTCCACTGGCTCCACAGCATGTTTTAATGGTTCCGGTTCTAGTATGGACACGTTAACAACAGATGGAAAGTCCGCCTCATAATCATCTCGATCTGTCAAGAAATCCAATTCCAATTCCAAAAAGTTACGGCGGGACTCATGATTGCTTGTTGGAACTACCATTCTTGGACATTGAACCTGAGCATCTGCGAGGGCTGTCCTTACTAGATTAAAGTTTGGTCTGAAGTTTGTCATGGACCAGTTCTCGCTGAGTCTGCCAGGTTTCTGGAGTGTGTTAGAGTAACTCATAACACAGTGGGACTCACAGGCAGACTTCGATCTCCAAACAGATGAAAGAACAGCCATGAAATGTTTCTGGAGAAGCAATTCATTGTTAGGAAGCTCGCTGATTACATTGAGCAACATCTGAGTTTGATCCTCAGATACTTTCAAGATAGCCTTCCCAGTCCCAGAAGGAACCTTCTCACTGTTTGAATTGTCTGTTGCTGATAAGATGTGCTTGCAGACTAATTCCCGGAATCTCTCACAGCAATGCACAGGGTGACGGTATCTTCCTCTATAAAATGCACCACCTGGTACAGAATGAAGAGAATCACTAGCCAGTTCCCAAAGAGGGCCGTACTCATTTACAGTTGCACAAAGAACAGCATCTTCCTCAGTTGTCCACGAGTCTGAAGCACAATCGCGAGACCATAGGCTCTTCTTCTTCAATCTCTCAGGCTTGATTACCATGACACGCTTTACTGGCATGCATGGGACAGAAATTCGGCCATCACTCTTAATTCTTGCCCCCGATTTGGGATCAGAATCATTAAGTTCATCTTTCAACTTAAGCTGCTTGCCTTCAAGAAAATGCTTAGGTGATAAGGCCTCGGAACTGAAACTCGATTTAGGGGCTTTCTTGAGCTTCTTCAGGCTTCTGCTATTGCTGTTCTCTTCCTCATTGGTTGACATTATCCTCTTATGCTTGTTAGAATGATGGTGTGCTGATTCATCGCTCATTAGCTCTGGTGAGGGTGCATTGTCATCAATGCTCATAGTATCTACTGATGTTTCCTCAACCATAACCTCTGACTCAGATGATAAACGTCCTTTCTTCAAAGATTTGAACTTCGCTGCCTTCTTCTTGTTCTTTTTTGACTTTTTTCGTTGAGTGCTATTATCATTCTTTTCCTCCAACTCTTTTGCTGCTTCACGGGCTTGTCTTTCTTGTTCCTCAAACAACTGTTTTTGAGCTAGAGCCTCAACATGTTGCCGATATGCTGTAGTAGCAAAATCAACATCCCATGACTCATAAGAAAGTGGTTCCTGGTCTTCATCAATTTCTGCTTCTAAATCTTCTTTGAGTTTTTCAATGCGTTCAAGTTCCCATTCTTCCTCTTCAACATTGACCTGATAGTTTATAGCAGCTTTATCAATTATTGGATCCCAGAGTTCCAAAAACCGCATGGCATATCTATCAATTGGCCGGAGCTGATTTTCAAAAGACGAACTTGCTTGACCTGCTGCAGCAGCTGCAGCAGCCATCTGCTTAACATCAGCAAGCATGTCAATATCTCCATCTCCTCCAGCCAAAGTTATAGCCTTTTCTTCATCTAATTGATTTATAGATAAAGCAACATGCTTGTCCTTGACCAAATCAGAACACTGATATTTATGCTCTTCATTGGTGTGTTCATCAGGTTTAGTGTCATCCTCGTTTACAAGATCATCCTCCTCAAGTCTTCCAGCAGCCTCCTCGCTGAACTCTTGATTGTCCACGGCCTCTTCCTGCTCCAGCCTCTTGAGAGCCATATAGTCAGCTTCATCTTCTGCCTGTCTAATAGCTGCTTCAACATCAACATTTGACAGCGCCAGATTAGTTCCGTTTGAGGGTCCAGCAGACAGAGAGCAATCCTTCTGCTGATTCTCTGCATGAAGTGATGAGTGCCCAGAAAAGAATTCCATAGGATCAAGCTTCTTGAAGAACTCTGTATTGTAGCTACCGCGTTGTATCACTAGATCATCAAGAGCTCGCTTCTGATTGGCTTTCTTGAGTATATTCTCCTCTATAGTGCTCTCACTGATCAGTCTATAGATGTGAACTTCACGAGTTTGACCTATCCTGTGGCATCTGTCTTGGGCCTGTTGGTCCATTGCAGGATTCCAGTCACTATCATAGAAAATGACAGTGTCTGCACCTACTAGGTTGATTCCCACACCACCACTACGAGTGGATAAGATAAAAAGAAAAAACTTTGGGTTAGTATTAAACCTCTGCATCAGTGTCTGCCTCTCTTCTGGCTGGGTTGATCCATCTAACCGCAAATACGTATACCCATATAGATTAATGAACTCCTCCAGTATATCAAGCATCTTAGTCATCTGAGTAAATATCAAGGCCCTGTGTCCTTCTGACTTCAAACGCCTCAACAAAATAGCAAGTTCCTGCAACTTTCCACAGTCAAACTGGATCAAACGCCTGTCAGGAAAGTACACTTGACGGCGAACAATCGCAGGCCTTATAGGAGAGAAAACAGGAGAAAACTCATTCATGCATTTCTCTCTGTATGCTGGTTCAATAAGAACAGGAGATTTCCCTTTGTTGCACCAGAATAATGGTGCAGGCGCTCGTGCAGCAGGAATTGCAAAAGTAAATGACTCAATAAAATCAAGCATTGTCTTGAAGCGATCCACCGATGATAGAACAAGATTTGCTAGGCTTGATGAAAATTCCATGTGGCATAAAGGGTTCTTCTTCTTCTCGAGAATATCAGACACAGGATGCTTTATGGTCAAAACCTCCCGAATATTTGTGCCATAAACAGGCCTCTTCTGGCATCTTACCCTATTCCACCATGCAATGGAAGCTGCTCTTTCATTAGCTTCTTTTATTCTCTCCTCCCACAAAGAATTGTGAATCTCTTCAAAAATATTTGTCCCATTGCTTCTCTGACCATCATTAGTAGAGCGAGAAATGCCAGAACCCCTGAGGGTTATGCTTGGAGAAAAAATGGCAGCAACCTCATCTTCCTCCCAAGAAGTCATATTATATTCATTTTGAGTAAATACAAAATTCATATCTGACAGGTCAACCTGAGAAAATGGGCCTTTATCAAGGACCATGCCAACAGAAGAGCTGATTTGCATGTTGATCCCTGCCATGTCAAAAGAGCTGATAATTGGACGGCCTTCAAAAAGATCTGGATGGTTACAAACCTTTCTAAGCTGCATAATGATGCTAATCATGCCAAAATAATTTCCACTTGCCAATGTTGCCTGTGTCTCTGAGCTTGCAATGAAATCTTCATACAAGTTCCTTTGCCTTCTGGAAAGTCGGCAATATATGACATGCTCATGCTTCTGTGGCAACTGTTTCTCCACATCCCGTTTCAATCGACGAAGTATAAACGGACGAAGGACGTTGTGCAACCGATCTATCACTTCTTTGTTTACCTTGTCTTGGCCCTCTACCATGCCTGAAATTGGATTGCAGAACCAGTCCTTGAACTCTTGATGTGACTGAAATACATGAGGCATCAAAAAGTGCATGAGAGACCAAAGTTCCATGAGGTCATTTTGTAGAGGAGTTCCAGTTAAAAGAATGCGTCGCTTCGAATTAAAATTTAGTAAAGTCTGCCATCTTTGTGATTTCCAGTTCTTTATCAAATGAGCCTCATCAAGAATAAGATACTTCCATTTTTTTCGCTTAAACACTTTGGAGTCCTGAATAACAAGCCTGTATGTAGTGATGCATACATGGAAGTAATTTGGTTTCATCCAACCTTGACGTTTCTGTTTTCTCTCTTTTGCACTTCCAAAATATGTCAGTATTTTAAACGCAGGACACCATTTGAGAAATTCAGTCTCCCAATTTAGCATAACACTAGTTGGCACTACAATAAGATGTGGACCCCATATTCCCTTCTCACATGCAAGGTGTGCTAGCAAGGAGATGGTCATAATTGTCTTCCCCAAACCCATTTCATCTGCTAGAATTCCATTCAGCCTCTTTTCATACATAGCAACAAGCCAGTCCAGTCCAATGTGCTGATATTCTCGTAGAGAATGCTTAAGAAGGAAAGGGAATTTTGTCCGCACATTTGTTGTTGAGAACGTGTTACCAGTCGGTTGTGCTGATCTTGCAGCAGCTGCAGCATCAGCAATCACATCACTATTATCTCCATTGGCCATCGCTTTAGTATCAGTTACATCACCCTCTTTAGCAGTATTTTCCTGTACAATAGGCTCTGATGTTTCTAGTTGTAGAACACTACCACTGACATGCTCAGGTCCCAGCATGCCTGCAGATTCATGATCTTCAAATGTGTCATTGTTGCCCTCCACAATCTCTGCAGACTGGTCATTATTCACTTTTACGGTCTCTGCAGACTGATCTCTGGTCAGTTTCATGGTATCTGCAGAAAGATCCCTGTTTACCTCCACGGTGTCTGCAGACTCATCATCCACAGGCATGTTGGCATTGACATCCTCAACTGATAGTGCAGGTGAATTTTCCAATTCTGTTGTGTCATCATCTGCATAGCCATCCTTTTGGTATCTTGCAAGAAGTTCTTCAAGTGGGATCTCACTCTCTTTCTGCAGTAACTTAACCTCATCTAGAGGATCACAGTCTTCTTTCTTCGCCAACTCTTCCTCTTCAGACAAAGTAGCTTCATCATCCTTTCCTTCATCATTAGCAACATAATCTTCGTCGTCCTTTGCATCAACAGATGAGATATTGCCATTGCATTTCACAGTGTTCTTTTTCACAAACTCAGAGTAAGACTGGTAATCATCTGCTTCCTCAGAAGAAATGCCTTCATCACTTGAAGTATGATCAGATTCATCGTTGCATCCATTAGCCTGGTTCAAAGGATCTTTAATCAAATCCTTTGAATCTGAGTCACTAAAAACGTCTCTGCCATCTGGACTGCTTTCCCTGCTAACTTTATTTTTAGTGTACAACTTGAGAATATCATCCAGTGGTAGATCAGCTTCTGCCTGCAAAGCAGCCAATTCCTCGTTGCGCTCAGCCTCCGTAATTTGAGCTTCATCCTCATCGATTGTGTGTTCATCATCTTTTGGCTCTTCACCCAAGGAACTGTTGTAATCATCATCGATTTCCACATTGTCAACATCAGTCGGACTTGATGCATTTATGTTCTCTTGTGCTAGTTCCTGCTGGGATCTTTGATTAGTCTGTAAAGAGTCATTTTCTTGATTTTGAAGGCGCACATCAACAAGATTTTCTGCCAGCATTGTTGAATATCTTTCAGTCTGTCCTAAGAGGAAATCAAGTTGCTTGTCTAGGGCCTTTTTTTTCCTTTCCTCAAGCTCCAGTTGGTTCTTATAAAAAACCAGCTTCTCTATTTTGGTCCAGAACTTCTTCACGTCCTTAGAAATATTTAGGGCAACTTTTCTCAGGCGAACTTCTTCCTCCTTCTGTTTTCTCTCGTCCTTTGTTGCTTGGTCAACTACACCCTTATTAGCTCTTTGAGCAATCCTTTTAGCCATGGACAGCTTCCATTTTCTCTCAGCATCAAACTCCTTTGCCAGCCAAGCCATTTCTCCAAGAAGATGGTCCCAGTGAGTTTTCGTCCTTCGAGGCTCCCCCCTTGGGGCTTCAAGAGCCTTCTGGCGTCTGGCTCTTGTCTCATGATCTAACTTTGATCGAGGACCTTTTGATGCCATCTTTCCGATATTTTGTAGAGAACTATCTCATGTCTTGGGGCATATTCAGAAAAATCGTATACAAACTCGGCACAAACCCTCTGAACCAGAGAGGCACCCAAGCGTGGCCCCGGGGTTCAAATCAGAGAGGGGCCCACCCACCCCAAGCGCCCCACCGGCGGCGACCGGCGGTGCGGCCTCGCGGCGGCGAATGGCCCCGTCAGGGCCAGCCGTCGGAGGGGATCTCGGGCGAGGGCCTCGGGCGCCGGCGGAGCAGGTCGTCACCGGCGAGCGGCGCCGGAGGCGGGGCGGCGGCGAGATCGGGGGAGTCTAGGGCACGGGGGTTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.946911
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0179500.2 2 28293836 T A
Osa02LNT0179500.2 2 28293837 A G
Osa02LNT0179500.2 2 28295616 G C
Osa02LNT0179500.2 2 28295826 G A
Osa02LNT0179500.2 2 28296151 A T
Osa02LNT0179500.2 2 28297111 A G
Osa02LNT0179500.2 2 28298520 C T
Osa02LNT0179500.2 2 28299028 A G
Osa02LNT0179500.2 2 28301085 C T
Osa02LNT0179500.2 2 28302058 A G
Osa02LNT0179500.2 2 28302843 C A
Osa02LNT0179500.2 2 28303318 A G
Osa02LNT0179500.2 2 28303579 A G
Osa02LNT0179500.2 2 28303774 A G
Osa02LNT0179500.2 2 28303816 G A
Osa02LNT0179500.2 2 28304822 C A
Osa02LNT0179500.2 2 28305643 A G
Osa02LNT0179500.2 2 28306193 A G
Osa02LNT0179500.2 2 28306258 G C
Osa02LNT0179500.2 2 28306334 C T
Osa02LNT0179500.2 2 28306829 T G
Osa02LNT0179500.2 2 28307207 A G
Osa02LNT0179500.2 2 28307210 A T
Osa02LNT0179500.2 2 28307709 A C
Osa02LNT0179500.2 2 28303239 G A
Osa02LNT0179500.2 2 28298317 C A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0179500.2 osa-miR5533 Translation 5.0 13.207 1 21
Osa02LNT0179500.2 osa-miR5794 Translation 4.5 17.989 1 21
Osa02LNT0179500.2 osa-miR5801 Translation 5.0 14.877 1 24
Osa02LNT0179500.2 osa-miR5143b Cleavage 4.0 21.367 1 24
Osa02LNT0179500.2 osa-miR5819 Cleavage 4.5 8.806 1 21
Osa02LNT0179500.2 osa-miR5820 Cleavage 4.0 11.15 1 21
Osa02LNT0179500.2 osa-miR5830 Cleavage 4.5 12.108 1 24
Osa02LNT0179500.2 osa-miR6255 Cleavage 5.0 6.31 1 22
Osa02LNT0179500.2 osa-miR396a-3p Translation 4.5 13.915 1 20
Osa02LNT0179500.2 osa-miR396b-3p Translation 4.5 13.915 1 20
Osa02LNT0179500.2 osa-miR399d Cleavage 4.5 12.656 1 21
Osa02LNT0179500.2 osa-miR399j Cleavage 4.5 12.656 1 21
Osa02LNT0179500.2 osa-miR399k Cleavage 5.0 12.656 1 21
Osa02LNT0179500.2 osa-miR156k Cleavage 4.5 13.08 1 21
Osa02LNT0179500.2 osa-miR168b Translation 4.5 18.725 1 21
Osa02LNT0179500.2 osa-miR169i-5p.2 Cleavage 4.0 12.832 1 22
Osa02LNT0179500.2 osa-miR172c Translation 4.5 15.543 1 21
Osa02LNT0179500.2 osa-miR166g-5p Cleavage 5.0 14.598 1 21
Osa02LNT0179500.2 osa-miR166g-5p Cleavage 4.5 12.987 1 21
Osa02LNT0179500.2 osa-miR396e-3p Cleavage 4.5 21.989 1 24
Osa02LNT0179500.2 osa-miR530-3p Cleavage 5.0 18.741 1 21
Osa02LNT0179500.2 osa-miR530-3p Translation 4.5 18.913 1 21
Osa02LNT0179500.2 osa-miR816 Translation 4.5 18.405 1 20
Osa02LNT0179500.2 osa-miR529b Cleavage 4.0 13.08 1 21
Osa02LNT0179500.2 osa-miR529b Cleavage 4.5 11.656 1 21
Osa02LNT0179500.2 osa-miR1850.1 Cleavage 4.5 16.147 1 21
Osa02LNT0179500.2 osa-miR1428e-5p Translation 4.0 17.692 1 22
Osa02LNT0179500.2 osa-miR1428e-5p Translation 5.0 17.288 1 22
Osa02LNT0179500.2 osa-miR1861b Cleavage 5.0 22.385 1 22
Osa02LNT0179500.2 osa-miR1861f Cleavage 5.0 22.385 1 22
Osa02LNT0179500.2 osa-miR1861i Cleavage 5.0 22.385 1 22
Osa02LNT0179500.2 osa-miR1861l Cleavage 5.0 22.385 1 22
Osa02LNT0179500.2 osa-miR1428f-5p Translation 4.0 17.692 1 22
Osa02LNT0179500.2 osa-miR1428f-5p Translation 5.0 17.288 1 22
Osa02LNT0179500.2 osa-miR1428g-5p Translation 4.0 17.692 1 22
Osa02LNT0179500.2 osa-miR1428g-5p Translation 5.0 17.288 1 22
Osa02LNT0179500.2 osa-miR396f-3p Cleavage 4.0 21.989 1 24
Osa02LNT0179500.2 osa-miR1862f Translation 4.5 15.168 1 20
Osa02LNT0179500.2 osa-miR1862f Translation 5.0 15.654 1 20
Osa02LNT0179500.2 osa-miR1862g Translation 4.5 15.168 1 20
Osa02LNT0179500.2 osa-miR1862g Translation 5.0 15.654 1 20
Osa02LNT0179500.2 osa-miR3979-3p Cleavage 4.0 12.29 1 20
Osa02LNT0179500.2 osa-miR3979-3p Cleavage 4.5 19.477 1 20
Osa02LNT0179500.2 osa-miR5143a Cleavage 4.0 21.367 1 24
Osa02LNT0179500.2 osa-miR5148a Translation 4.0 12.634 1 24
Osa02LNT0179500.2 osa-miR5148b Translation 4.0 12.634 1 24
Osa02LNT0179500.2 osa-miR5148c Translation 4.0 12.634 1 24
Osa02LNT0179500.2 osa-miR5156 Translation 3.5 9.127 1 24
Osa02LNT0179500.2 osa-miR5156 Cleavage 5.0 19.571 1 24
Osa02LNT0179500.2 osa-miR5490 Translation 4.5 20.777 1 21
Osa02LNT0179500.2 osa-miR5503 Cleavage 3.5 15.747 1 22
Osa02LNT0179500.2 osa-miR5507 Translation 5.0 10.369 1 21
Osa02LNT0179500.2 osa-miR5513 Cleavage 4.5 6.979 1 21
Osa02LNT0179500.2 osa-miR2275c Cleavage 3.5 9.098 1 23
Osa02LNT0179500.2 osa-miR5523 Translation 4.5 16.158 1 22
Osa02LNT0179500.2 osa-miR166j-5p Translation 4.5 13.511 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0179500.2 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0179500.2 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0179500.2 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0179500.2 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0179500.2 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0179500.2 2 nan Morphological trait Seed C747 C1445
Osa02LNT0179500.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0179500.2 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0179500.2 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0179500.2 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0179500.2 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0179500.2 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0179500.2 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0179500.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0179500.2 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0179500.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0179500.2 2 nan Physiological trait Eating quality nan nan
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