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

>Osa03LNT0240300.2

TGCCATTGTTGCTCTTTGATGAGCCTTTGATGAGATCAAATATGGCCTCATGATGCTTTTGTAACACAATGTACTCTATTGCTATCTGAGGAGCAGCAAGCTCACAACATACAGTACAAAACTGCCACCCATTTTCATTTAGAAACTCAGTAGAGTGGTATTAGTAAAAACTCAATTAATCTTCAGACAGAAATATCATCTAAAGTTGCGCAAACAAAGGAAAGCAACCTCAGGCTTCTCGTACTCAGGATCAGGAATGATTCCTTGTCGTCCCAGGCTGTGTTTAGATCCAAAGTTTGGATCTAAACTTCAGTCCTTTCCCATCACATCAACCTTCTTGGCTTCAGGATCCTTCTTCTTCTTTGGAGGAAGATTATCACAATCACCATAGATGCTTCCAGTTCGCTTCTCAGTGTTATCAATCAGAATGCTGTATTTGGCGTCAGGACGGATGATCAAGGTGTAGACGTGTGTCAGTTGATCGGTCTCGCATGGCACGTCCTTCTTGATCAGATGGTTATTGCCGTTCTTAGGCTCGTTTTGCGTACCTTCCCAATCTTCTCTATCTCCTTCTCCTCAAACACACCCTTAGTAAGGATAGCGTGAACCTTCTTGGTGGCATACCCGCAGATATCTGGTCCAAACATGATGCTGTACGGTGTCTCGCCACCAAACTTCTTCTGGTCAACATCGCCGCCAAGCAATTTCACGTAGCCGCCGCCGCAGTCGAGCTTCTGCTCGTGCTTCACCGAGAACTGCAGCACGAGGGTCTTGTCCTTGTTGCTGAACTCAGGGTACTCGGCCGAAATGGCGTAGAATCTGTAGTCCTCTGATGTCTGGATACCCTTGTTGTTGGTGTCGCCGTTCCACTTGCCGGCCGTGTGGTTCCACTCGCCGACTGTGTTGTCCTCCTTCTTCCACTCAGATTTGACCCACCGATCCTCCCATCCATCTTTAGCTAAACACTTTATCTCAACTATAGCTATACCAGTTCCAGACAGGAAATGTACAGGGGCAAAATGGTCAATTCTCAAAGTGAGCAAGTCACTATAATCCTCCTCATCGGCATAACATTGTTGGAAGCAATCGAGCAAAGTGAGTGGTACTATTAAATTCTTTTCGTCCTCTGTCTTCTCTGATCTTAGCATCTCTTCGTTCTCCTCTGTTCATCCCCTCCTTCCACATGATTAGCTGATAACCACGCTTTCCACGTGGTTTCCTTTGGTCAGAGGGGCAAACAAATCCAACAAATTGTGTCATCGAACGGGAGGCAAATGAAGCGTAATGTAATATGATGGTTCCGTATTAGATTGGACCTAATGAATGTGGACAATAGATTTTCTAGCCTCACTATCCCTAATGTTTATGGTGCTATTAAAATCTACTAAGATAATTCTTATTTGCTCCAGCAGTGTATAAATAGGAACCACTTGAAGAATTTCATTTTTTCCATTCAAGTCTATAACTCTCAAAGTTACATTGCCATGTTCATGCTTCTGAACTGTTTCTTGAATGATGGAATGGAGTAACCACCAGTACTGTCTCCCAAGCCGTTCAAAATAAACCTAAACTGAAGCTGGAATAGCATCAGAACAGTCTCCTTTTCTGATACCACATAGTACTGGATATTTTTGTCTGGGGGTTGAATTGATGGATAGGCTATCCTCCAAGTGTTTGAATTCTGTTCAAGAGGTTAGCAGCGTGTAATCCTGCAAAAGGACACTTGGCAAGATATTTTACCCAGTAGACATAAACTAGTTGTATTCATCATTCACCAATAATCTTCACAAGAGCATTTTCCATCCTCAAACTTATGCAAACACTTTGGATCCTTGATCAGTATATGGCGTCCATATTTCTCTGAAACTAGTTTGGCAAAGGTGTGGCAATGGTTACACATCCTTGCAGTTTTGATTATCCTTATGTTTTTGAACTGTGGGGAATTAGAAAGCCCAAATGCAATAGCTAGCTTCTCACAATGGACTCCAACAACTTCTTCCTTTTCTTCTTCAACATCTAGAGTTCCAATGCCAATGTCAAGCATAGAATGTCCCATCTTAAACATCATCGACTTTAATTCTGCTACTGTATCCTCCAAGCCAACATTATCACCATTTGAGAACACATACACCTTATTCCTGATTTCTATTGAACAGCTCTCGACCTCATCTAAATTTCTTCCTTTGTTGGGTGTCATCTCCTCTGGCACATCAACAGTTTTTCCAGTTAGATCTTGCAGACTAGAACCTAACCTTTGGACTCTGGGATCTCCAGGATCAATCGCAGACAGTTCTCTAGCTGCCAGGTGAGCCAGTCTTACATTTCCATGCATTACAGCTGCAGTAAGAAATGTGTCCCAGACTGTTGAATTGGGTATCAAAGGCATCTCGTCAATAAGCTCATATGCTTCTTTTAGTCTCCCTGACCGACCAAGAAGATCCACCATTGCTGCATAATGGTCTAATTCTGGAGTTATATTGTAATCATTGGCCATGTTGAAAAATGTCTGAGACCCTTCAGATACCTTTCCCGTGAGACCATAGGCCTTGATAACAGTGACCAAAGTTGTATGATCTGGCACAACACCTTCTTGCTTCATTTGACAGAAAAGATCCAAGGCTTCATTTGGAGAACCATGCAGCACATGAGCGAGAATGATACAGTTCCAAGAAATAATGTTCCTTGATGAATGCATATCAAACACAGCACACGCACTAGCAAGATTACCAGATTTTGAATATGCATTGATAAGTGCATTTGCAATTTTGCCATCCAGTTCTAAATTGTGGTGAAAAATACAGGCATGGATCTCCCGTACTTTCCAGGACGCAACTAGATTTGTGAATGCTGGAATAATGCTAAGGATGGTAATGTAGTCAGGCCTCCTCAGAAGTGCCTGCATCTGCCGGAATATTCTTATGGCTCTATCATAATAACCATTATGCACTGATCCAGCAATGAGTATGTTCCAGGTTGCTGTATCCCTTTTTACTCCATGACTTTCCATCATCTGGAATAGCTCAAAAGCTCTCTCATCATCCCCATTCCGTATGTACCCTGAGATCATTGTATTCCAGGTTATCACATTGCGCCGAACACCATAGTTTTCCATCTTACAGAAGAGCTCGTATGCTTTGCCACAATAACCTGCTTGTGCATACCCTGAAATCATTGAATTCCAGGAGAATATATCCTTGTCAGGTATCCCACTAAATATTCTCCAAGCTGCAACTATTTCTCCACATTTTGCATACATGTCAACCAAGGAGTTCCCTGAGAGCACGTTGTTAACACTGCCAACCTTAATAGCATGGCTATGGAGCTCCTTTGCCTGGTTTAGTAACTTCAAACTGGCACAAGCTGAGATAGCACATGCAATTGACATGCCGTTAGGTTCAACTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.854486
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0240300.2 3 33747325 C G
Osa03LNT0240300.2 3 33744626 T C
Osa03LNT0240300.2 3 33744783 A G
Osa03LNT0240300.2 3 33744937 G A
Osa03LNT0240300.2 3 33745662 C T
Osa03LNT0240300.2 3 33746751 T C
Osa03LNT0240300.2 3 33746803 T A
Osa03LNT0240300.2 3 33746819 T C
Osa03LNT0240300.2 3 33747542 A G
Osa03LNT0240300.2 3 33744338 T C
Osa03LNT0240300.2 3 33749419 C G
Osa03LNT0240300.2 3 33748088 T C
Osa03LNT0240300.2 3 33745968 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0240300.2 osa-miR5538 Cleavage 5.0 20.793 1 22
Osa03LNT0240300.2 osa-miR5542 Cleavage 4.5 14.094 1 21
Osa03LNT0240300.2 osa-miR396a-5p Cleavage 5.0 22.02 1 21
Osa03LNT0240300.2 osa-miR396b-5p Cleavage 5.0 22.02 1 21
Osa03LNT0240300.2 osa-miR396c-5p Cleavage 5.0 22.02 1 21
Osa03LNT0240300.2 osa-miR398b Cleavage 4.5 19.121 1 21
Osa03LNT0240300.2 osa-miR171b Cleavage 4.5 19.245 1 21
Osa03LNT0240300.2 osa-miR171c-3p Cleavage 4.5 19.245 1 21
Osa03LNT0240300.2 osa-miR171d-3p Cleavage 4.5 19.245 1 21
Osa03LNT0240300.2 osa-miR171e-3p Cleavage 4.5 19.245 1 21
Osa03LNT0240300.2 osa-miR171f-3p Cleavage 4.5 19.245 1 21
Osa03LNT0240300.2 osa-miR815a Translation 2.0 6.021 1 21
Osa03LNT0240300.2 osa-miR815b Translation 2.0 6.021 1 21
Osa03LNT0240300.2 osa-miR815c Translation 2.0 6.021 1 21
Osa03LNT0240300.2 osa-miR1432-5p Cleavage 4.5 15.061 1 21
Osa03LNT0240300.2 osa-miR1442 Translation 4.5 18.617 1 20
Osa03LNT0240300.2 osa-miR1858a Cleavage 4.5 10.407 1 21
Osa03LNT0240300.2 osa-miR1858a Translation 5.0 8.234 1 21
Osa03LNT0240300.2 osa-miR1858b Cleavage 4.5 10.407 1 21
Osa03LNT0240300.2 osa-miR1858b Translation 5.0 8.234 1 21
Osa03LNT0240300.2 osa-miR1865-3p Translation 5.0 22.387 1 24
Osa03LNT0240300.2 osa-miR2876-3p Translation 3.0 14.846 1 21
Osa03LNT0240300.2 osa-miR2880 Translation 5.0 23.581 1 24
Osa03LNT0240300.2 osa-miR1862f Translation 3.5 12.268 1 20
Osa03LNT0240300.2 osa-miR1862g Translation 3.5 12.268 1 20
Osa03LNT0240300.2 osa-miR5486 Cleavage 4.0 17.168 1 21
Osa03LNT0240300.2 osa-miR398a Cleavage 4.0 19.121 1 21
Osa03LNT0240300.2 osa-miR2873a Translation 4.0 23.945 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0240300.2 3 nan Morphological trait Panicle/flower G249 RG418
Osa03LNT0240300.2 3 qSBR-3 Resistance or Tolerance Sheath blight resistance G249 G164
Osa03LNT0240300.2 3 qPES-3 Morphological trait Panicle/flower G249 G164
Osa03LNT0240300.2 3 QFll3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0240300.2 3 QSn3 Morphological trait Culm/leaf G249 RG418
Osa03LNT0240300.2 3 nan Resistance or Tolerance Drought tolerance R1618 G164
Osa03LNT0240300.2 3 Qbp1 Resistance or Tolerance Insect resistance R1925 R2443
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