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

>Osa03LNT0196300.2

TAAGAATAAAAATATAGGAATTTTCCATATCAATAATATAATTGCCACAAAAAAAACTTGTCCATTCATCTGGTACAATAATGGTGGGAAATCACCAAGTAATGAAATGCATGAAATTCAGCTAAACATCAAAGTCTCACACCTGAAAATACAGTATGGAAAGCGTTGCATTCCTGAAAGAACTGCAAACATCATTACCACAGAACCAAGAGCTAATGATACCATTACTCTCGTGAATTCCATTTATCCACTTGTCCACAAGCCTGAAACCCTGGGCCATTGCGGTAGAAAGGATAGAATCCTCATCAACTCGGCGCTGAATGTAGCAAAGAATAAGGGCTGCATCTGAATCCTTATTAGAAATTAGTTCCCTAGCAGTCTTGAAGAGGGGAAATATAGCGTCAGGATTGTAGGTAACGTCAGTTCCTATTATGCAATCAAAACCTGCTCCATCGCTGGAAAGCTCCCTGACTGCCTTCAGATCATCTTTGTCGCCCCAAAATAACTTCCTGATCAGAATCTTTTTAAGCAAATCAGGCTCCAAGTTAGAGGCAGTATTTTCTCTAAGAAGATCGAGAGATTCTGCGTCTCCATCAGTAGCTACAACAAACTGAGCAACTGTAGCAGCAACCATTGAGCAGATGCCAGCCGAGCCACAGCCCAGTTCCAGCACTCTTTTGCCAGCAAGAATGGAAGGATTCTCTGCTAGAACACTGCACATGAATTGAGCTGATTCCCAAAGCATTAGACCGGTTAATTTGCAGGTGTGCTGGTGTTCTTTTGTGAGCATTTTTATTTCGAAGTCATGACCTTTTGCTTTGATCCGAAGGACCTGAGCCTGCAGTTAATTGCTGCTGGATGCATGCCTTGCCAGTCATCGGGTAATTGTATTGCTTACCAATGACATGGATTGAAAAGGACAAATGGGCTTTTTTTTTTGTTCTTCCTTTTTCTTTGCAGGTAATCCACACCTCATCAAGGTTGTGTGAAGTTCCAAACATATTGTTAAAATCCTCAGAAAGGTCAATTTCTTCACTGGTGCTCTTCTCCTGAGAAGCATTAGCAGTTAACTTATCCTTTTCATCTTCACAAGTGTGGGAATCGTGCTGGCCATTTGGGCCTTGAAGACCAGCTGAGCCAAGGATAAAGGTGGCTTGGATCCAGTTCCTGTTCATCACCAAGTCAAGTGAGCGGTTCTCGACTTGTTTATTGTGCACACAAATCTCCTCAACAGTAAATCCACATGTTGAGAATAAATCCATCAGGTACTCATTTGAAAAGTAATATGCTCGCGTGCCATCCCCTCTGACATAGAAATTCTCACTTATTTGTTGGCCTTTAGACATAAGTCTTTCCTGTGCAAGGTCGCCAAAAGCATAGTCCCGAAAAAGCACACGGCCACCATTTTTCAGAACAGTTCTAACATTCTGAAGAACTAGAGGCATTTTAGCGGGTGCAACATTGTTACAACATCAACAGAGGAAGGTTGTACATTCTCAGTTAGTTGCTCTGATGTAATATCGCATGCAAATGCATTTACTCGGTCAGGTCTGTAGTCCTTATGTTTCTTAACCAAGTCAACAGCTCGGGGAGAAAAATCACATGCGTGAACAAATATATCAGGGTATGTAGAAATCAATGGAAATATTGTATTTCCAGCTCCACATCCAACCTCCAAAATCACCATCTTCCCCCCTCCTTGACCCTCAAAGTACTTTCCCCATTCTTTATCCAAGTAGTGTCGATCCTTGAAGAACCTGTCCTCGTGGCGCTTGTAGAAGATGTCCCAGTACCTCCTCGCATCCCTCTCGTACTTCTCTTTCCAGAAAGGCGTGACGAGCCTCCCGGAGGATGTAGAGGAGGCGGAGATCTGCTGCTGCTGCGGCTGCTGCTCGCCGGCGGCCATGGCGCTTCGCTTGGTTTGGAGGCTCCACGGCGAGGGTTTCCTGTTTCCTTCTTCTTCCCTGGCCATATGTGTTGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.92198
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0196300.2 3 2380535 A T
Osa03LNT0196300.2 3 2381149 C T
Osa03LNT0196300.2 3 2381273 C T
Osa03LNT0196300.2 3 2381534 A G
Osa03LNT0196300.2 3 2381847 T A
Osa03LNT0196300.2 3 2383446 G C
Osa03LNT0196300.2 3 2384527 G A
Osa03LNT0196300.2 3 2384620 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
Osa03LNT0196300.2 osa-miR5804 Cleavage 5.0 18.08 1 21
Osa03LNT0196300.2 osa-miR5823 Cleavage 4.0 17.233 1 24
Osa03LNT0196300.2 osa-miR397a Cleavage 5.0 20.226 1 21
Osa03LNT0196300.2 osa-miR444a-3p.1 Translation 5.0 17.665 1 21
Osa03LNT0196300.2 osa-miR817 Translation 4.0 19.05 1 21
Osa03LNT0196300.2 osa-miR1425-5p Translation 3.5 18.957 1 21
Osa03LNT0196300.2 osa-miR1425-3p Cleavage 4.5 18.06 1 21
Osa03LNT0196300.2 osa-miR444b.1 Translation 5.0 17.578 1 21
Osa03LNT0196300.2 osa-miR444c.1 Translation 5.0 17.578 1 21
Osa03LNT0196300.2 osa-miR444d.1 Translation 5.0 17.665 1 21
Osa03LNT0196300.2 osa-miR1850.2 Translation 4.5 21.813 1 21
Osa03LNT0196300.2 osa-miR1852 Cleavage 3.5 15.641 1 21
Osa03LNT0196300.2 osa-miR1860-3p Cleavage 5.0 24.995 1 22
Osa03LNT0196300.2 osa-miR2921 Translation 5.0 14.353 1 24
Osa03LNT0196300.2 osa-miR5515 Cleavage 5.0 15.32 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0196300.2 3 nan Resistance or Tolerance Drought tolerance RG348 RZ329
Osa03LNT0196300.2 3 qFDN-3 Physiological trait Flowering RZ329 RG348
Osa03LNT0196300.2 3 nan Morphological trait Root CDO20 RG409
Osa03LNT0196300.2 3 qHDD3-2 Physiological trait Flowering RG348 RM231
Osa03LNT0196300.2 3 qHEJ-3 Morphological trait Shoot/Seedling RM175 RM22
Osa03LNT0196300.2 3 qST3-2 Physiological trait Eating quality nan nan
Osa03LNT0196300.2 3 qDEF-3 Physiological trait Flowering R518 C721
Osa03LNT0196300.2 3 QSbr3a Resistance or Tolerance Sheath blight resistance RG348 RG944
Osa03LNT0196300.2 3 dth3.1 Resistance or Tolerance Drought tolerance RG104 RZ329
Osa03LNT0196300.2 3 qtl3.1 Resistance or Tolerance Drought tolerance RM7332 RM545
Osa03LNT0196300.2 3 QSs3 Physiological trait Sterility RG348 RG944
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