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

>Osa03LNT0196500.2

GGTTGGGTTGCTTTGCTTTGGGCGTTTCATGGTTGCGCTGTTTGCTCCATGTGCAATGATCTTACAAGTGTGTGTGCGTCCTTTTCATGTGCATTCACTGTAAGTTGGGCTCCAGTCATTCATAGCATATTAGCAGCCTCAATCACAACGGTATTTCACTTCAACGCTAAGAAGAAACTGAATTGGAAATCATGATGGATGTACATTAACAACGAGAATCTTAGATTTTATCAGAGAAACTAGCAAGATGAGAAACTGCGTCCTCAAGGCGCGACAAGTGTACAGCAAACCTGTCCTTCAGCTCCGCCAAGTCTGTTTCACTGAGAGCACTCCGCATGATCTTGAGACCGTTCTGTACAAGCATCATTCCTTCACAAATTCTATCTGGCATCTTCCTCTTCTTTGTTTCCACATCATTAGTAACTGAAACATTCTCAGGCATTCCTTCACAAATTCCATCTGGCATCTTCCTTTTCTTTGTTTTCACATAATTAGTAATTGAAACTTTCTCAGGCTCTGGAACTAGAGGAATTTCCAAGCATGATTCAACCAGTTTCTTCAGCATTCTCCCCTCTGAAACTAGTGAACATATTTGCTCTTCAGACCATTTGTCATCTCGCAAGGCTACCTCTTTCTGAAGGAAGGCTTTCAATTCTGACATAAACCCATCCTCATCTATGTCCACCCCTGTGCATGTGTAGGAAAGGGCAGCATCTACAGGAACAAATTTCCAGAGCTGTGCAAAAGAAGTGCGAGCGGCAAAGTACCCAAAGGAACCCATTGCAAGGTGAATGAGTGCCCAATGCCGCTCCCTCAGCAAGAAATGGAACAGATCCCACATTGCAGAACAAAGTGGGTTTGCATCGTCTTCAGTAGTGTTCAAGTGACCAAGAATTGCCATAAATGAAGCCATTGATGGTTTGCACTGAGAGATTGCTGTATTTGAATTATCAAAACTGGACATGAACAGAGTGTGCAACTCCAAAGTTAACTTCTCCAACTCACTGAACGCACAAAGATGCCTCATGTGCGTAATAATAACCAATATGGAACTGATGTGCTTGACAAGGAGGTTCTTACTGCTATCAGGTGAAGTTCTATAAAGATTAATGAGAGAGGTGGCAATCTTGAACATAGTAGCAATACTTTTTTCATCAATGGTAACGTCCTTTATTTCGCAACTCTGGAAAGCAGAGGCTAGAGCATGTACAGGAAACCCTATTATGCCCGAACTAGAAGAAGTTGGCAAGTTGATTTCTCCATGATTCTTGAAGTAGTTCTGATTCTGTAGATACCCAGCAAAAGAAGTGAACAGTGTCTTCACAGCATGTTCCTTTACACCACGAGATAATGAATCAAAAGGAAATCCTTCCATCAACAGTGCTAAGTACAAGATCGATGACTTGGAAGAGCTATCATTCAGCATGGTATAAATTTGATCAATTGTTGCAGACGATGCATAGCTCAAGATGTTACATGATGCACGAGCAAGCTTCCTCAGAGCACTGAGAGGTGCAAGAACTTCCTCTGGTGACGCTAGAGTCTTTAACAGAAGAAATAGCTGATTGATTAAATAGGTTGAAGTTTCAGCTTCAGCATAATGCATGAAGAAACACCATAGCTCTGTTAGAATTTCCAAGCAAAGGAAATGGGGATGGAAAAGGTTCTCAAGTAAGAAGACTTCAAACTCACTCCAAGCAGCACTTGAAGAAGAAGCAGCAATCATAAAAGTCTTCAAGGCTTGTATAAGAGAAGTATATACAGGTTGCCAGACAACCTTAGGAGAATCATCATCACTACTTAGTGCAGGAATTTGGCAGCCAAGTACATATGAGTAGACATCTTCCAACGTTAAAATATTAAGAAACAGATGTAGCTTCTTACATAATTCAATGACCACCTCTTCCCTCAACCATGGGGAAGCATTGAGGAAGTGCAAGAACACAGTAAATTCAGCAGGTAAAAGTGCCCTGTTTATATTATCAACATCAGAATCCACAGAAAAAATGCAACCCAATGTAGCGAAATTCATTGTATGATCAACTTCTCCGGTGTACTCTGGATTACCGGTTCGTACTTTTTCCAAAAAGTACTGCACGAGCTGGCATTTAGACTCTGGACTTACTTCTGTTGACTTCATAAGTGTGTCTAACAGAAGAAAGGAACTAGGCTCCAATAACTCAAAAAGTAATTCACTTGCTGCTTTCAACTGGGGATTTCTGCAGAACAGAATACTTGAGTGTGAAATCAGCAGTGCACACCGGATTATGCTCTTGTATATTGCCATTGTTTCAGATGGATATATAGAACAAATCCTAACGGCGTTCGTTAGGAAATATTTGATTGGTAAGAAAGCCCTTCTAGCTTCAGCGGTACCAAGGACTTCTTGTAATGGTACACACCATCTCTCAGTAGCAACCCTCAGAGATTCAATGGCAACTGAGATAGGAATTAAAATAATCTCTCTTACATTCACCTTTTCTTCTACCATCCCTTTACCAAGCTGCAGTAAGGAAATTATGCCCTTCCATGATATATTCAGTAAAATCACCTGGCTTCCACCACTGGATGCTGCATGGGTTCCTATTTTACACAAGGACTGAATAGTGCATGCTGTAATCTGGGCAATGTTGCTAGTAAGATCTGTCTCTTTGTGTTCCTCAGTTGTCTCTTCTTTAGGCATGCTCATTATGCACTGGTCTGATTTTGCAGCCTCGGAGTACACTCTGCACAGTTTGATGGTTTCATCTAGAAAAACAGGTGCAGCCTTAGCAACATGTCCTGTAGTTCCGAGTTTCTTGTCAAGTATTGAGCTTTCAGTCAGGGTTAGTAACTCCAAAATAAAGTCGCCAACAGCATGCACAGTATCTTCGGCAATGCATTTAGATGCAACAGGGAGGTGCTTGGAAGAGATATTTAAGGTCAGTGCAATTATCTCAGGAAATAATCTGGAGTGTTCTTCCTCTTGGGCATCTTCAGATTCATCAATAGATTCAACAGACCACAGGAGATGCCTCACACACCACGAACCAGCCTTTGAACCAAGAGTAAGAAATGGCCCCAAGCAATTGGTTGTATCTAATTCTGAGCATTTAAGAGCAACCTGCAGAATTGACTTGTGTAGCATGCAGTGTGATACACCGGAACATGTGGAATCATCCCACGATGCGATCAGACTTTCAACCACTAGGCCCAGATCATCTGCACACAACTGAAAAGGATCCTCGAGTTGGTTGATAAGGGAAATTCTGTTCTCCAAAACCTCGGAGGACTTGATGGCTTCCACGAGGGACCCGAGCTCGCTCCTCCTCCTCCTCTCCTCCGCCTCCTCGCCGGCGGCGCCGCCGTCAGCCTCCATTTCCCTCCCCCGTCTCGGCCGTGCACCTCGGCTTTCCCGCCTCCTCCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.975147
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0196500.2 3 2450316 C T
Osa03LNT0196500.2 3 2450636 C T
Osa03LNT0196500.2 3 2452027 A T
Osa03LNT0196500.2 3 2453680 T A
Osa03LNT0196500.2 3 2454168 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
Osa03LNT0196500.2 osa-miR5812 Translation 5.0 14.747 1 24
Osa03LNT0196500.2 osa-miR5836 Translation 5.0 17.958 1 21
Osa03LNT0196500.2 osa-miR171b Translation 4.0 14.469 1 21
Osa03LNT0196500.2 osa-miR171c-3p Translation 4.0 14.469 1 21
Osa03LNT0196500.2 osa-miR171d-3p Translation 4.0 14.469 1 21
Osa03LNT0196500.2 osa-miR171e-3p Translation 4.0 14.469 1 21
Osa03LNT0196500.2 osa-miR171f-3p Translation 4.0 14.469 1 21
Osa03LNT0196500.2 osa-miR426 Cleavage 4.0 21.287 1 21
Osa03LNT0196500.2 osa-miR390-5p Cleavage 5.0 21.088 1 21
Osa03LNT0196500.2 osa-miR1429-5p Translation 4.5 21.619 1 21
Osa03LNT0196500.2 osa-miR1849 Translation 5.0 17.221 1 21
Osa03LNT0196500.2 osa-miR1865-5p Cleavage 4.5 20.832 1 24
Osa03LNT0196500.2 osa-miR2094-5p Cleavage 4.5 16.06 1 21
Osa03LNT0196500.2 osa-miR2871a-3p Cleavage 5.0 13.69 1 21
Osa03LNT0196500.2 osa-miR2871b Cleavage 5.0 13.69 1 21
Osa03LNT0196500.2 osa-miR2876-3p Cleavage 5.0 18.298 1 21
Osa03LNT0196500.2 osa-miR5151 Cleavage 3.0 5.428 1 22
Osa03LNT0196500.2 osa-miR5151 Cleavage 5.0 7.386 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0196500.2 3 qHEJ-3 Morphological trait Shoot/Seedling RM175 RM22
Osa03LNT0196500.2 3 S34(t) Physiological trait Sterility nan nan
Osa03LNT0196500.2 3 qOE3-1 Physiological trait Eating quality nan nan
Osa03LNT0196500.2 3 qTA3 Physiological trait Eating quality nan nan
Osa03LNT0196500.2 3 QSs3 Physiological trait Sterility RG348 RG944
Osa03LNT0196500.2 3 qDEF-3 Physiological trait Flowering R518 C721
Osa03LNT0196500.2 3 rn3 Resistance or Tolerance Drought tolerance RM231 RM175
Osa03LNT0196500.2 3 QSbr3a Resistance or Tolerance Sheath blight resistance RG348 RG944
Osa03LNT0196500.2 3 qtl3.1 Resistance or Tolerance Drought tolerance RM7332 RM545
Osa03LNT0196500.2 3 dth3.1 Resistance or Tolerance Drought tolerance RG104 RZ329
Osa03LNT0196500.2 3 nan Morphological trait Root CDO20 RG409
Osa03LNT0196500.2 3 qFDN-3 Physiological trait Flowering RZ329 RG348
Osa03LNT0196500.2 3 nan Resistance or Tolerance Drought tolerance RG348 RZ329
Osa03LNT0196500.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0196500.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
Osa03LNT0196500.2 3 nan Resistance or Tolerance Drought tolerance RM231 RZ329
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