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

>Osa02LNT0180200.1

CTCCAAAAACAATATAGAACAATAATTCCCAATTCCAATTCAATCGCACATTAAGTGGTTCACAAATCATCTCAATGGTAATTAAGTTTGTAAGATATGCTATCACAATCAATGGTATGTTTATGATTTACAAGACAATAAACATCATTGATCTACTGAGTGGCTTGCTCCTGTCATCCTGTGAGGCTCGCATGTATTTGCAATGAGGAAAAACAACCTGAGAATGGATTACACCAAAACCTGTCCATGCATTTGGACTTGAGCTAGAACCGGGAAGTTGTTAACAGTTGGCTATTGGTGAAGTTAGCATATGGAGAATCGGGTCTGGCCTTCCCAATCTTCTTTGCCCTAGAATGTGTATCTTCACGTCCTATATTCTTCTTTGGTGTTAGATCATGCACCTCTCTCTTGTGTCCAACAACACTTTGCAGTGCATTATCAATGCTATTGTGCTTGAACACCTCAGTTAGTGCCACCGAATTTCCTTGGTTAGCTGAGTTATGTCTCGCAATAGTCGACACCTTAGAGTGTAGAGCTTGACCACTTGGATGCATTAGATTGTCACGTGGCCATGGGATGCATCGAGCTTGAGCACTTCCTAACTTGCTGATCATTCCATATGCACGAGGTATTATGGTGTGCTGATTGAATACAATGTTAACAAGGATGTCAACACAATCATTTAGTGCCTGGCCATCAACAGAAATAGCGTTTTTGTCGGTCTTCTGAATGGTACCTAGAGCAACCATTTTTCCACTTTTTGGAGATATTAGGCCAACTTTCATACCACTTTTCAAGATAGCTTTTGTATCTAATCCAGCCTCCAGCCCTTCATGGAGTGGTGTATGAAACTGTCTTTTTCTGTTTTGTAGATTGGGTTCAGATGAAGTTGGTTTCTTTGATTTCTGTTGGACAGCATATGAAGGTGGTATATTCTCCTTATTCAAATCTAGCCGAGGGGATCTAAACTTCTTTTTTGTTGAGGAGGTGATGTCACTTGACCAAAAGGCTCTGACTGTTTATGCAATTCTAGATGAGGAGATCTAAACTTCTGTTTTTGCTGAGGAAGTGATGTCACTTTACTAGACGGCTGTGACTGTAGAAGTGTTTTCTTGTTTCTGGATGAAAGTGATGGTGCTTGATTGATGCAATTCATAGGATCCAGTTCCTCCAACTGATTTTTAGCTGGTGAATTAGACACCTGACTTCTATTCATAGGTGCATGCCCTTGGGAAGCTAGCAACATACTTTTTAATTCCTCATATTGTTTTTCCAGCCTTTCATTCCGTGCCATCATCAAGGTCTGATTTGCTGCTAATGTGTCCACCATATCCAAAGCTCCTTGTTCTCCTGTTTAGTTTCTTCTAGTTGTGCGATAGCTTCAGCTAGGTGCCTTGAAGCCACTCCACCTGCTAGCAGGCCCATGCCACTGTTCTTTCTAGTTTTCTTCCTTGGAAACATTTCTGAATATAGATCATCATCTCGTGCCTCTTCACCGATATGAGCAGGGTTTTCCTCGATCCTTCTTTTAATCAATTTTATCACTACAGTATTCATCCAAGGGTTCTCCATTTCTTTTGGTATGAGTAATTACATAGAGTTCAGCCCGTCCAACTTTTCTGTTCTCTTTAAGCTCCGTTTGATCAAGAACAACTGCAAAACCTCGTGAACCAGTGGTGTGAGTTCCATTGAGTTGCAAGGATCTAGTAGCTTTATTCCTCTCTGACTTGATCCGAGCTGCTTCAGTCTTCCAATACCTCACCAACCATGCCCATTGTTTTATAGGGATTCTTTCTTGGCAGCCATTAAGTACATTTTGTCTCCATGATAACTCAGAATTGAAGTACATTCTCTTCAAGACAGCTTTAAAATCTTTCCACTTTTTGCTAGCTGATTTCAAAATCCAAGGTTTGTAATGATCCTCAATGTCAAAAATTCCCTGAACAGATGTCCAAACTTTCGTCTTGCTTGCTTCAGGTACCTTTCTCCAATTCTTTGCAGCCAAGGATACATATTTGCCTTTGACAAGAGTTCCAATAAAATTGGTTAATTTGCAAGTCTTTAATCCACAAGGTTGACCATATCGATTGAATTTCAATCTGATCTTCTCATTGGGATCAAGGTCCTTCCATAGCGATCTCATCATTGTGGGGCCTCTTCCACTTTTCTTTGTACTTTCATGAACTTGACCTTCATGCTCCAAGTCAGCATAAGGTGGCAAATTGTCCCCAGGTTCAGTCTCATCATAATCTTCAGAGCTACAGTAATCTTCATAGTCATCTCCCTCATCGGATCCTCCATTGCTTATTATGTCATCTTCAGTTTGAAAGTTGTGTTCATATGTGTATCCATTTGCATCATAAGGCAGATTGCAACTATGTGTTGTAGATTAACAATGCAGCATAAAACAACTTAGGACAGACATTCAGAAGTGCACATATTCAGATTAACCTGCAAATGTGTCATTTTGTTTGGATGCCAATGGCATTGCAGCATGAAAGTTTCTTGATTTAAACTTTGTTGGTTGGTGATCAAGTTCTCTGAATTGGATAAGGCGAATTCTATAAATTTATCAACCCCGATATTATATTCAGCACTAGATCTAGATGTTTTCATCCAATCCTTATCCATGGTAAATTCAATTAATATTACAGTATAAAGGCAGCAACGGTAGATCCCAAGGTGGCTCGGCTCGACCAGGATGAAGAAAGTGGAGGCGCGACTCCGGATCCAGCAGGGAGAGACGGCACCGGGACTGGAGATGGTGCCGGCGGAGGGAGCAGCAAGCGCCCCCCTCCCCCCGACGACTACCCTAGCTTGTTTGAGGCGCAAGTGATCTGCAAGTTTTGGGCATGGAACGGGAGCGAAGCAGGCTGGTGTGTGTAGATCTGGGGAGTAGAGCGGCGGC

Coding Potentia
Explanation CPC Score
noncoding -1.06536
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0180200.1 2 28627775 C G
Osa02LNT0180200.1 2 28626478 A G
Osa02LNT0180200.1 2 28626914 A T
Osa02LNT0180200.1 2 28628151 T C
Osa02LNT0180200.1 2 28628152 T G
Osa02LNT0180200.1 2 28629865 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
Osa02LNT0180200.1 osa-miR5528 Cleavage 4.5 18.368 1 21
Osa02LNT0180200.1 osa-miR5541 Cleavage 5.0 22.233 1 21
Osa02LNT0180200.1 osa-miR415 Cleavage 5.0 21.4 1 21
Osa02LNT0180200.1 osa-miR426 Cleavage 3.5 16.509 1 21
Osa02LNT0180200.1 osa-miR1425-3p Translation 4.0 21.492 1 21
Osa02LNT0180200.1 osa-miR1853-3p Translation 4.5 18.736 1 22
Osa02LNT0180200.1 osa-miR1854-5p Cleavage 4.5 16.263 1 21
Osa02LNT0180200.1 osa-miR1869 Translation 4.5 12.602 1 24
Osa02LNT0180200.1 osa-miR1878 Translation 4.5 17.973 1 24
Osa02LNT0180200.1 osa-miR2094-5p Cleavage 5.0 18.546 1 21
Osa02LNT0180200.1 osa-miR2105 Cleavage 4.5 16.3 1 20
Osa02LNT0180200.1 osa-miR2105 Translation 5.0 14.359 1 20
Osa02LNT0180200.1 osa-miR5071 Translation 4.0 24.54 1 21
Osa02LNT0180200.1 osa-miR5144-3p Cleavage 4.5 18.08 1 21
Osa02LNT0180200.1 osa-miR5161 Cleavage 4.5 12.769 1 20
Osa02LNT0180200.1 osa-miR5491 Cleavage 5.0 15.521 1 21
Osa02LNT0180200.1 osa-miR5499 Cleavage 4.0 11.884 1 21
Osa02LNT0180200.1 osa-miR7692-5p Cleavage 5.0 19.793 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0180200.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180200.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180200.1 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0180200.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0180200.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0180200.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0180200.1 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0180200.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180200.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0180200.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0180200.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0180200.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180200.1 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0180200.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0180200.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0180200.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
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