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

>Osa03LNT0239200.1

CTTGTTCCAATGTTACACTGTCCCTGGAATTCAGATATGCTTAATCTCTTTCATTCTGACTTGACAAGGTAGCCCGCCAACCAACCACTTGGTTCATTTTGATTCCAGATTTCCAGTCAAGAACATGTCATAGCTAGATGATGATGATAAGCATAGAAGAAGTGTATCCCTTTCCCCTCGAAAAAGCATAGAAGAAGTGTATGAATATATATGGGTTTAATTCGTTATGGAGAACTGGAAGAAAAGTGTCAGCATCTGGGACCATGGGGATCATTTTGAAAGACAAGTGACCCCTGCAAATTGCAGTCTTCCTGGAGAACTTGGGCAATTAGGGGAGGAAATCTGAAGGCAAAGTCGCTTTCAGCGCAGCCGTTGTGCTGCCTCATCCATGGACAAGAGATGATGGATTCAGACGGCATAATCTCCAGTCAGCCATGGAAATCATCCAGGCCTTATCCGTCCTTGATGTGTTGCCTCCTATCCCCACAGGAATAGGAATATGGGATAACTCATTCCAATCGCTGTCTTTTCAGCAAAATTGGAGATGCAATTCTGGGACAGCTATTTCAGACAGTTTCTGAGCTACCTTCTTTATTATTCATCTGTATGTTAACAGAAGGATAGTACTAGAGTGAGATACAGTCATGATTCATGAATCATACAAGAAAATACTGGATTAAAATGCTATGCAATTTAATCAGACAAAAAAAAACGATGTACTGCCTTCTTGTTGGCTTGCATGGGTGGAGGCATGGAACCGCTCATCTCAAGGCATAGCAGCCTTCATGTTCTTGGCATACTCTTCTACTCTTTTCAACCCTTCTTCAGGTGAAGCAGCCTCTCCTAACTGTCTAACAATAGCGCTGCCGATGATCACACCATCTGCTCCCCAGCCTGCAATCTGCTTTACATGCTCTGGAGTCGATATGCCAAAGCCAACAGCAACAGGTTTGTCTGTAACCTTCTTGATCTCCTGAAGAAGGTACTCAACACGCAAATTTACATTTGAGCGTGCACCTGTAACTCCAACAGAACTTACAAGATAAATAAATCCTTCTGAAGCTTTTGCAATCTCCTTCATCCTCTCTGTTGGTGTGGTTGGTGTTGTAAGCAGCACCAGCTCTATGCCATGCATGACAGCCTCATTCCTCAACAGCGCTGTCTCTTCCAAAGGAAGATCAGGTACTACAAGACCATGTACGCCGGCTTGTTTAATGATAGCCATGAAGTTACTCACTCCGCGCTTTAAAATTGGGTTGTAGTATGTGAAGATAACTATTGGACAAGACAACTCAGGTATAACCCCCTTGAGCATAGCTATGACGGAATCAAATGTAGCGCCTTTCTTAAGAGCACGCGTTGCTGCAGCCTGAATAACCGGCCCATCAGCCAACGGATCCGAGTAAGGTACACCCAGCTCAATCACATCTGAACCACAGGAATCAAGGATCTTCAACGCTTTCGATGTGGTTGCCAAGTCAGGGTCACTGGCGGTGATGAATGGAATGAATGCAGTCTTGCCCTGCTCCCGGAGCCTGGAGAAGGTCTCCGCGACGCCGCGCTTCCCGGCGCCCACGACGCCGCGACCGCTATCTTCCATCTCCATGAGCGGCAACCTCCCTGGCTCCCTGTCCCTGGCCGACAGGCCCAGCCCCGCCCCGCCTCCGCCGCGGAAACGAAGCAGAGCAGCCCACGCGGAGGAGAGAGACGCCGCCGCGGCGGCGACGGCAACGGCGACGGCGACGAAATGGAGGCGGCGGAGCGGGTGGCCTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.953239
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0239200.1 3 33194137 A G
Osa03LNT0239200.1 3 33195470 G T
Osa03LNT0239200.1 3 33196579 C A
Osa03LNT0239200.1 3 33196970 T C
Osa03LNT0239200.1 3 33197263 A 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
Osa03LNT0239200.1 osa-miR5788 Translation 5.0 21.289 1 21
Osa03LNT0239200.1 osa-miR408-5p Cleavage 4.0 24.251 1 21
Osa03LNT0239200.1 osa-miR414 Translation 5.0 20.264 1 21
Osa03LNT0239200.1 osa-miR815a Translation 3.0 18.81 1 21
Osa03LNT0239200.1 osa-miR815a Cleavage 4.5 19.421 1 21
Osa03LNT0239200.1 osa-miR815a Cleavage 5.0 14.035 1 21
Osa03LNT0239200.1 osa-miR815b Translation 3.0 18.81 1 21
Osa03LNT0239200.1 osa-miR815b Cleavage 4.5 19.421 1 21
Osa03LNT0239200.1 osa-miR815b Cleavage 5.0 14.035 1 21
Osa03LNT0239200.1 osa-miR815c Translation 3.0 18.81 1 21
Osa03LNT0239200.1 osa-miR815c Cleavage 4.5 19.421 1 21
Osa03LNT0239200.1 osa-miR815c Cleavage 5.0 14.035 1 21
Osa03LNT0239200.1 osa-miR2120 Translation 5.0 16.824 1 24
Osa03LNT0239200.1 osa-miR5510 Translation 5.0 16.42 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0239200.1 3 nan Resistance or Tolerance Drought tolerance R1618 G164
Osa03LNT0239200.1 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
Osa03LNT0239200.1 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0239200.1 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0239200.1 3 qSBR-3 Resistance or Tolerance Sheath blight resistance G249 G164
Osa03LNT0239200.1 3 qPES-3 Morphological trait Panicle/flower G249 G164
Osa03LNT0239200.1 3 QSn3 Morphological trait Culm/leaf G249 RG418
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