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

>Osa02LNT0180300.1

ACGGGATACAGAGAAAAACTACATTGTTAACATCAACTGGTGTAATAGTTATGATATATTACATCGAATTGCTACACATGCTTATAAACAGAACATACAGTCGAAGAAACTATTAATTCTTTGGACAGTAAATAACAGGCAAATCTGAATATAACTGAGGGGATTATACATGACATCAGAGAAACTATGAACTATTGACTATGAGATGAATGCATAAGATTAGCTAAATAGACATCCTAAAATGCTGAAGTTAGTACTTTACAGGAGACAGCTATGCCAAAAGCCATTTTTATAGTCACCAACACTGTTGCTCTGCAAAGAATTTCCCCTCCATGGAGTCATTGGCTCAACTACTGTGTGAGAACCAAGAAGCACTCGTGATGAGAGCCTAAAGGGTCTCAACCTCCAGTTAGAAATATACAGGTGCTGTTGATCTTTACATGTCATGTCACCACTGCTAATTAGTTATCAGCTGTTCCCAAGTTATATTGAAGTAACCATGCCATTTGCTCTTTACTGACTGTAGCCCAAATGACTGAAAAGCCCGCATCTTCGATTAGCTGGGAATGTACACGAAACTTGCAGGTCCAAGGCTAGCAAATCAACACCAGATACATTTAACATCACAGTTGACGCCTATGAAGGATCTCGCAAGGCAGGACTAGCCATTCTAACACGGTGAGCAACAGCCAGGGGCGGCCTGCCAACAGCTTCCAGTATCCTAGTAAAGGCAACCTTCGCAGGGACACATGTGACAAGTGGAATTCCCCCTGGTTTGATCAAGCCGCCAAAAATGCCACTCTGCTTATGTGCTTTTGCTTGACCACCTACTCCATGATGCTTTTTTCCAGTGGAAATGGAAGAGAGGGTTCGGACCTTCTGGCTTGACAGGCTTGCTTTTTTGGATTGCTTCTTTTGAGATTTAGAGGCTGACGGCCTCCTAACATTTGAGATGCTTTTCTTATCAACCTTAACCTGATGATTTGAATTTGAGTACTTTCTAAAATCTGAATTTGAGTACTTTCTAAAATCTGGTTTCATCTCCCAGTCTGGATATGCAAGGGTACCTTCATCATCACAATCCAATGCCCCTGAGGGGTTAGATCGGGGAATTCTTTGCATGGCAGTCCTCCTGCCTGTACACCAAGCAGGTTGCCCTCCAGTTCTCCCTTCCAAACTAACATCACCACAAAAAACCAGGTGGTCAGTGGAACCATCTTCAAGTATTTCAATTTGAACAGGATGCCCAACAATTGCTTTGCCATTCAGTCTGCTCATTAAGGAAACAAGAGGAACATGCTCTCCCTGGTAGCTAGCCTGGACCTTCAAGTCAACATCAAACAACATTGGGCCCCTGCCACGAAGACGTGAACTGTACTTTTGGTAGAATGAGGGTCCGCTCCAATATGCATTCCGATCAAAATGAAATATCTTATCTGAATCCCTGTTTAGGGGAGAAACCTTGGAAGAATCATTTCCATAGTCGTTAAAATAGCTGTAGCTTCGGCTAAAATCTCTTGTAGCCTTCAAACATGAAGAATATGTTCTACCATGGTACAAGTTAACCTCTGAATGACCTGTGTCCTCAAAAAAATCTGTTTCTTCGGAATCGTAATTGACCTCTTCGTTTTGGTAAAAATTTTGCCCCAGCAATTGCTGATTGGGAATTTGCATACTCCCTTCTCTGGGATTTCTACCATTTATTTTATACGGAGATCCTTCCATGAAACCATCTGATTTGTCTAACCAGGGATTTCCATCTGCCATATCCGATCTCTTAGGTGCATTACGGCTATTACGTTTACCTTTCATATGCCATTGGGAGACGCCCAACTCAGAAGAGCCATCCTCTTCTGATTCATTCACTTGACACATATAAGAAGAATAGGTCAGCTCATCAGCATCAGCATCAATATTCGCATGCCTGAACTTGTCAGAAGCTGGTAAGAAATAAGGATCATGGGCATGTGATGCTGGATGCAGAATCAAATCCGAACATTGTAAAAGTTCAGCGTCATCTTCTGTCTCACTCTCAGAGCATTCCCTCTCTGAAGACTCATATATGTGCTTCTCAACAAGATCAGAAGATGTCTGCTCCTCAGAAAAAGCAGGATGATGAAGATAACTTTCAGTCTCAAAATCACCTCCTGTAGAAGCCACTTGTACGGAAGGTAAATCACTATGACTATGAGTTTCACCAGAATCAGTAGGTAGGAATACATATCTACTTCTTTTAGCTCGGTAATTGGCAGGTGATCGATCCATTTCTCCCTGAGTTAGGACATCCCCATAGCCATCATTGTGCTGTGACTGATGAGGCAATTTTGGACTGCTGTGCAAAATCTGAACCAGAGGTTGGCGTCTGTCACATTTTTCAATAGATTCATCAAAATCACTTCCATCTGATCTAATCTTTTCCGCAGTTGTGATTTTCTCCTTGCTATCCAAATTTTCTCCGGCCTGTATATGCCTCACATGCGAGATGTCTCCCAAGTGATTGCCAAAAAGATTATCAGAAATGCCCCGAGTAGGAGAATCTTGAAAGTTTCTCTTTGAGCCAGCATGGAGGACATATTGCTCAGCTTCCTTTTTTATATCAGAAGAAGCAGTTATGCCCTTCCGTTTCTTACTCTTTTTGCTCTTGTAGCGGGTACTTCCAAGATCTTTGTTATGTTTAGAGCAAACTGCATTTCACAAAGATAATTGAGGTTTTATATCCAACATACTCCCTTGAAGATCATGCAAACAATTTAGTCAACAATGAAGGAAGCTAAATCAAACTTTGCCAATAAATGGGCTTACCAGAAACGTTAGCAGGTCTGGAACCTTGAGTCTGATGCTTTGATGCAAGCAGCTTCTTCTCCAATTCAAGAGCATGAAGAATAGCATCTTCTCTACGTGCATACTTCTCTCTTTTCTTAACAGAAGTCCCTTCAGTAGCCTCTGCCTTCTCAATACATGCATCAAACTCCCCACACCTAAATGCTTTGACGCGCTTTGATTTTTCAATGTTGTACCAGTCGACACTGGCATCCTCACGGCCGAGAAGCTTGACCGGCGTGCCGGACCTTGGCGACATGATCTGCGACGGCGGCAGCTCGTCGGGCCCCAGAATCCTGCCGGGCCACCATGACCCGTTCCTCCGCCGCACCCACACAATGGTCCCCGGCGAGGTATCCCCAACGCCGCAGCAGGCCACCTCCCCGTCTCCTCCTCCCCCCTCCGAGCACCCCGCCATCCCTCCCCCGGCCACCAAACCAAGCCCTAACCGCCGCCTCGCCTCGCCTCGCCTTGCCTCACCCCGCTTCTAGAAGCTTCCCTCCCTCTCGAGATCTACCCTCCATTCAAATCACGGAGGGCGCCTGCATCTAGAAGCCCTCTCCTCCGCGCTCGCTAGATCGCCCTGCCCCTCGCGCTCGCTCAGCGCCCCCCCCCCCCGGCAGCTTCTAGAAGCTTCTCAGCGAGGATCCCAAGGAGAGCCGCCGCCGCCGCCTCCTCACCCCCCTTCCCCCTCCTTCTCCTCCTCCTCCTCCACCTCCGCGAGGCAGGGCCCCTCCGGCGGCGCCGCTGGTTCGCTGCCGCCGAGGCGGTCGCCGGAATATTTTTTTCCCTCCTCTTTCTACGACAGAAAAGGGTGGGAAATTAAAGGGCAAATAAAAGGATT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.979216
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0180300.1 2 28797164 G A
Osa02LNT0180300.1 2 28796986 C G
Osa02LNT0180300.1 2 28797777 G A
Osa02LNT0180300.1 2 28798053 T A
Osa02LNT0180300.1 2 28796157 C T
Osa02LNT0180300.1 2 28798766 T G
Osa02LNT0180300.1 2 28799348 A C
Osa02LNT0180300.1 2 28799674 C T
Osa02LNT0180300.1 2 28797395 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
Osa02LNT0180300.1 osa-miR6246 Translation 4.0 22.088 1 23
Osa02LNT0180300.1 osa-miR396a-3p Translation 4.5 17.279 1 20
Osa02LNT0180300.1 osa-miR396b-3p Translation 4.5 17.279 1 20
Osa02LNT0180300.1 osa-miR166i-5p Cleavage 3.5 15.419 1 21
Osa02LNT0180300.1 osa-miR1846a-5p Cleavage 5.0 10.576 1 21
Osa02LNT0180300.1 osa-miR1846a-5p Cleavage 4.0 19.07 1 21
Osa02LNT0180300.1 osa-miR1846a-5p Translation 4.5 18.644 1 21
Osa02LNT0180300.1 osa-miR1846b-5p Cleavage 5.0 10.576 1 21
Osa02LNT0180300.1 osa-miR1846b-5p Cleavage 4.0 19.07 1 21
Osa02LNT0180300.1 osa-miR1846b-5p Translation 4.5 18.644 1 21
Osa02LNT0180300.1 osa-miR1846c-5p Cleavage 5.0 10.576 1 21
Osa02LNT0180300.1 osa-miR1846c-5p Cleavage 4.0 19.07 1 21
Osa02LNT0180300.1 osa-miR1846c-5p Translation 4.5 18.644 1 21
Osa02LNT0180300.1 osa-miR2121a Translation 2.5 11.206 1 24
Osa02LNT0180300.1 osa-miR2121b Translation 2.5 11.206 1 24
Osa02LNT0180300.1 osa-miR2919 Cleavage 5.0 10.57 1 19
Osa02LNT0180300.1 osa-miR2919 Cleavage 4.5 8.433 1 19
Osa02LNT0180300.1 osa-miR2929 Translation 4.5 12.418 1 21
Osa02LNT0180300.1 osa-miR5339 Cleavage 5.0 20.132 1 21
Osa02LNT0180300.1 osa-miR5498 Translation 5.0 19.736 1 21
Osa02LNT0180300.1 osa-miR5535 Translation 4.5 15.156 1 22
Osa02LNT0180300.1 osa-miR2863b Cleavage 4.5 15.816 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0180300.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180300.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180300.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0180300.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0180300.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0180300.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0180300.1 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0180300.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0180300.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180300.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0180300.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180300.1 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0180300.1 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0180300.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0180300.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0180300.1 2 nan Physiological trait Eating quality C621 C370
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