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

>Osa02LNT0173500.1

CGACACAACTATGATGTCATTGGCCTCTTGGCAAGCATGGGGTTCAACCAACCATTAAAAGTTGCGCACTTGCGCCTAACATCACAACTACAGCATTTTTATCTTGTCTACAACCCCTAGTTAAAACCGCTACATGCCCAATCAGTTGGCATTCCAATAGGTCACCCGACCGAAGAGTTACAACCACACAGGGTGCAATGTTTTAACACCTTTTGAGACTAAGCGAACCTTTTGAGTCTAGAGAGCGAATCCATGTACAAGAGAAATTAGCGGGTAACTTCAAGCCTTCCTTCTGCGCTTCTTTTCTCCAGTAGAAGCGCCACCAGCGGATCCCTAACTTCAAGCCTTCCTTCTGCGCTTCTTTCCTCCAGTAGAAGCGCCACCAGCAGATCCCCCCTGCTCCACTTCAGCTGCTGCCTCGCCTTCTGCTTCCTTCTGCTTCTCTTTCTCAGCTGAGACATTGGCCTTAGATTCCTCACCAGCCACCGCAGCACCGGCAACCTTTGGCTTTCGACCTGGCTTGGCTCTTCCTTCACTTGGTTTGCTCTCACCCTTCAAATCCTTGCCTCCGCTGCTAGCCTCCTTTGGTTTACTGGCACTCTTGTTGCTACCATCCTCAGGCAAATCATCCTTTGTCTTCTCAGTTGACTTAGTGGCTTTGTCTTCGGATCCTTCTTCAGCTTCCTTCTTAAGGTCACTGCCAACCTTAGGTGTCTCATTTTCATCCTTCCTTGCAGCTTTCCCCTTTGATTTGCTTGAAGTTGCCGAGATGTTACTTTTGGGTGTACCATTGCTGGAACCTTTCGGACGACCCCTTTTTTTGGGAAGATCGCCTCCACCACTTTTAGGTGTTTCTGCATTTCCTTCCTTCAATTGCACTGAGCTCCCTCTTCCTTTTCTGCCCCTACCCCGTGGCTTCGGGGAAATCTCGGAAGCCACATCAGGGGTTTTGTCTTGTTCCTCACTGACGAATTCCCACTTTTCATCCCTAAGGAGAAGCACCTCTACATCTCCATCATCATATGCAATCTTGTGCCTTTTTGAAGCTGTATCAAATGAGTCAACAATGCCCTTGTAAAACTTCTTGTCGTCAGGCCACCATACTTGGATCCTTGCACCAACAAGGCTAGCATCAAGGCCTTTATTCTTCCTAGAACGAGGAGTCTCTTGTTCATCCTCTTGTGACCTTTTCCTCTTGGAGCCATTATTGTCCTGGCCTTGGCTGCCCTTGGTCTTAGCTGACCCCTTGGACACGGACTTTGGAGAGACCATTTCCTTTATTGAGATAGAACAAACAGTACAACAACCAGTGTGCTAAAAAGCAACTGAATAGATGCTATTAAATTCTATCTGTTTTGAATTAACATCAAAGATAGGATCAAATCACAATTGAACCACACTAAATAACTCCTATATACTCAGTGTTATAGCAAAGTTTACAAGACAATAACAGGATTTGAATCACAAGCAACTGTATCAGTAAACAAAAGCTCGTAATACCTTGAAACAGTAAACACACTCAAAACATGTTTCAGATACACAAACATAGCATGCCAGAGAGAAATAGTATTAACAAAGACTGAATAATGCAGCAAATCAATGCTAAAGACAGGCAGCTTTACTAATTATACAAAAAAATTACTACTGACAAGAAAATTACCTTTAGGCTCAGATCCTTAGCAGTATCTTCCTTGGAGTCAGTTTCATCCTTCTGTTTCAAACTGATCTTTTGTTGCTTTTTTGATGACCCTGCTCCACTTGCCTTTCTTGTAGATGACTTGGAATCATCCTTAGATGACTGCTTCGATAACTTCCCTGTTGAATCAGTAGTCTCCTCAACCTTTTTCAGACCTAGAACTTTCTTTCCAGCAGCCTTCTTCTCCAATGACTTTAGTCCAGGAGGTCGACCTCTTTTTGATTTGACCATAGCTGGTGAGCCATCAACACGTTCTGATGTTTCAGCAGAAGCTCCATTGGCAACCTTTGCTGACTGCTTAACACCATCCTTTTTCTCTGAATCGGGATTGGATAATTCCTTGGGATTAGCAGCTGCAGATTCTGTGCCATTATCAACTGGAGTTGCACCACTGCCAATAGCAGTAGTCTGAGTAACATCTTGCTCCAACTTTGCAGGTTCCTGAGGTAGCTCATCAGAAATAGTCCTTTCAGAAAGTTTGCCATCATCCACCACATCTTTTCCAGAAGGATCAGCATCCATGTCTTCCTTGACATCTGAACTGTCTTCACAAATTGTTGCGATAATATTGTCATATTCATTCAAGGAAGTGCCTTTAAGTAACTGCAGAAAGACCGGTTTCAGTTTTTCAGAGCATGCACCTATCACCTTCTCTGCAAGTTCAAAAGATGCAGCAGAAGTTTCCTTCAGTTCGGACTTAGCATGCTTGAGCAGACATTCTGCAATGGGTATCTCAACTTCATCATCCTCTTCAATTACCAAAATCATTATTGTAGTCATACAGTTTGTAACATTTTCTGGGTGATTTGGTTTCACAGTTGTGAAGAAGTTGTGAAACATTTGCAGTATCAGATCTTCACACTCAAGATCCAACATCACCACGCATAGCCGGACCTTTGCCACAGTTTCAAGGATTGCAACTATCCTTCGAAACAAGGGGTTCTCCATATCATCCAATTTCTCAAAAGACCCCACCATTATGGAAAACACGTCCTTCATGACATCATCGTCATATGGAGTGTCAGGTGCAGTGATCCTAGTTATCTCAGAAATACAGGACACCACAGAAAGTTTCACCTCATAGCTAGAATTATCCAACAGCTCTTTCTTGATCAAAGCTTTCATTGCTGGAGTTATAGCACTAATCATGCTTTCAGAAGGTGCTTGTTCCACTTTCAATATATATATTTCGGCCTCGTGGATGAGCTTGAGCAAGGCATCGACGTCGTCGGGGGGAGACTGGAGCTTCTCCCCGACGTCCCTCAGCTTCCCCTCGAGCTCCCCGAGCTCCGCCATTCCCGCGCGCGCGGCACCCCCCGCGCGTCCCCCCCCTGCCACCCCCTGGATCCGGCCGCCCCCGCCCCGCCCCGCCCCGCCGCGCGAGATCTACGGCTTGCTTGCTAGGGTTTCAGCGGGGAGGGAGGAGCAACGCCGCGCACCACCCCCTGCCCACGCGCGCGCGAGGCAGCGGCCGACGCCGACGACGGCAAACCAAGGTGACGGGAAGAGAGGAGAGGAGATGGATTTCTCTATAGCTATCTCTGCCTCTCTCTCTCTCTCTCTCCCCCAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.154383
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0173500.1 2 24140187 G A
Osa02LNT0173500.1 2 24140218 A G
Osa02LNT0173500.1 2 24140342 A G
Osa02LNT0173500.1 2 24140492 A G
Osa02LNT0173500.1 2 24140642 G T
Osa02LNT0173500.1 2 24140776 A G
Osa02LNT0173500.1 2 24140995 A C
Osa02LNT0173500.1 2 24141187 A G
Osa02LNT0173500.1 2 24141193 A T
Osa02LNT0173500.1 2 24141275 C T
Osa02LNT0173500.1 2 24141481 A G
Osa02LNT0173500.1 2 24141545 G A
Osa02LNT0173500.1 2 24141770 C T
Osa02LNT0173500.1 2 24142014 C A
Osa02LNT0173500.1 2 24142270 T A
Osa02LNT0173500.1 2 24143008 T C
Osa02LNT0173500.1 2 24143061 T C
Osa02LNT0173500.1 2 24143143 G A
Osa02LNT0173500.1 2 24143560 A G
Osa02LNT0173500.1 2 24143561 G A
Osa02LNT0173500.1 2 24143688 C T
Osa02LNT0173500.1 2 24143702 A G
Osa02LNT0173500.1 2 24143928 T A
Osa02LNT0173500.1 2 24144047 G A
Osa02LNT0173500.1 2 24144071 A G
Osa02LNT0173500.1 2 24144146 C T
Osa02LNT0173500.1 2 24144198 T C
Osa02LNT0173500.1 2 24144240 G A
Osa02LNT0173500.1 2 24145023 A G
Osa02LNT0173500.1 2 24145215 A C
Osa02LNT0173500.1 2 24145221 T C
Osa02LNT0173500.1 2 24145257 G A
Osa02LNT0173500.1 2 24145340 T A
Osa02LNT0173500.1 2 24146183 G A
Osa02LNT0173500.1 2 24146402 A G
Osa02LNT0173500.1 2 24146706 C T
Osa02LNT0173500.1 2 24141600 G A
Osa02LNT0173500.1 2 24144268 A G
Osa02LNT0173500.1 2 24142876 T G
Osa02LNT0173500.1 2 24144199 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0173500.1 osa-miR1861o Cleavage 4.5 16.822 1 22
Osa02LNT0173500.1 osa-miR160a-3p Cleavage 4.5 16.384 1 21
Osa02LNT0173500.1 osa-miR160b-3p Cleavage 4.5 16.384 1 21
Osa02LNT0173500.1 osa-miR160d-3p Cleavage 5.0 16.384 1 21
Osa02LNT0173500.1 osa-miR396c-3p Translation 4.5 12.204 1 21
Osa02LNT0173500.1 osa-miR159a.1 Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR159b Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR159c Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR159d Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR159e Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR159f Cleavage 5.0 21.624 1 21
Osa02LNT0173500.1 osa-miR319a-3p.2-3p Cleavage 4.5 21.656 1 20
Osa02LNT0173500.1 osa-miR319b Cleavage 4.5 21.656 1 20
Osa02LNT0173500.1 osa-miR1428a-3p Cleavage 4.5 13.851 1 21
Osa02LNT0173500.1 osa-miR169r-5p Cleavage 4.5 9.847 1 21
Osa02LNT0173500.1 osa-miR1855 Translation 5.0 18.345 1 21
Osa02LNT0173500.1 osa-miR1428b Translation 5.0 13.851 1 21
Osa02LNT0173500.1 osa-miR1428c Translation 5.0 13.851 1 21
Osa02LNT0173500.1 osa-miR1428d Translation 5.0 13.851 1 21
Osa02LNT0173500.1 osa-miR1861a Cleavage 4.5 16.822 1 22
Osa02LNT0173500.1 osa-miR2092-5p Cleavage 4.0 18.017 1 21
Osa02LNT0173500.1 osa-miR2863a Cleavage 5.0 16.31 1 21
Osa02LNT0173500.1 osa-miR5488 Translation 4.0 14.231 1 21
Osa02LNT0173500.1 osa-miR5506 Translation 4.5 17.586 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0173500.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173500.1 2 nan Others Others C424 G45
Osa02LNT0173500.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0173500.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0173500.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0173500.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0173500.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0173500.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0173500.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0173500.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0173500.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0173500.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0173500.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0173500.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0173500.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0173500.1 2 Tiller number Morphological trait Culm/leaf R26 C424
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