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

>Osa02LNT0178900.1

GCAGAACAAGAGTAGGGCTGTGTATAAGATTATGGTGCCATTTTGAGCATGAACAGCGGGTAACAATCGCTAGAGAAATCGTCCACGAGTTACTGCCAATGCCATGACGCTACACGGGAAATGCAAGGGGAACAAATCAACACATTTACTGCTGTTGAGGAGGCAGGACAAGTTTTATCTTTTCCCTTGGCCCGTCATGCTTGTCTCGTTGGTGCTTTCACATGCCTACTTGCCTTCTCTACCTTTTCTTCCCCACCATCCATCTTTTCACTTCCAGCTTTGCGAGAACAAGGTGACGAATTCAACTCCTACCTGATCAGTGGACACCGCAGAAAATCCTTGGGGATGCACACGACCAAAGCAGCACCAGCAGTACAACTGATCACAGTACGACTCTGCAGGTTGTGTCGAACGAAGACTGACTGCCTGCCTCTCTCATCTTTAAACCCAGCAGTTAATAAAATTGCCACCGTTTCCTTTTCCGGGGCCCCTGAATTGCGCAGGTCGCCTTCAGTGACGGTGCTGCTTCTTCTCCCTCCTCCGTCCGTCCTCAAGCTCTGCCCCCGTCCGTCCGTCCTCTCTCTTGCTTTGCTTCTTTCCTTGCGTGGTTCTTTCTTTCTGTCACTTTGCTGCCATCTTTTGCTTTCTCCCACTGTTGATCAAAGGAGGTTTGAACTTGAGCTCAGCTCAGGGGCAAGGCATCGCTCTCCGTTTCTTTTGCTGCGTCTTTCCTGGCTGCAATGGCTGGGAGCTTTGAGGGGAGGAGCCCTGCAGCTAGAGGAGTCGAGCAGGTATGCAACATGAAGCGTTTTTCTTTTGCATCTTCTTTTAAAGCATTGTGGTATATTCATGCTTATGCCAATGATTCTTCTTTTGCTCTCCTACAATTCCAACAATGCATCTTTGCTAAGTTGGATGGATTTGCTCTTCTTGTTTGTCTTCAAGGAGCCAATAAACACTGAAAAGGACATCTTCCTCCATTACGCGATTTAATTTTCTGGTTCTTTCCTTCAGGCGCTTGTTGCTCTGAAGAAGGGTGCACATCTCCATGTTCCGTTGAGCAGAGCCATGACCAGAACTCTTAGATGAATTCCGCCCAGTTATCCACTTCTCCTTCATCTATCTGCATATCAAGATCTCACGATGTTCCTCCGCAACCTTTCAAAGATGTTCCTTGTTTTCCCACCGCGGAGGGTCCAGAGCGGCGCCGTGACCTGATCGGCGCAGACGCCTGCGCGCCTCCCTCCGCCTCCGTTTCCTCCTCCTCCTCCCCGTTTCGGCTACTCGCCTCGTCGTTGCCGACGGTGGCGTGCCCACACCACCTCACCGCCGCCGCGCTTCGCAAAGGCGGATTCCGATATCATGTTGCGGATTTTGGTCGATCCGGTGTTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.194071
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0178900.1 2 28013685 G A
Osa02LNT0178900.1 2 28013884 A C
Osa02LNT0178900.1 2 28016931 G A
Osa02LNT0178900.1 2 28017006 A C
Osa02LNT0178900.1 2 28018328 A G
Osa02LNT0178900.1 2 28018871 C A
Osa02LNT0178900.1 2 28019616 A T
Osa02LNT0178900.1 2 28020469 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
Osa02LNT0178900.1 osa-miR160a-3p Cleavage 4.5 8.299 1 21
Osa02LNT0178900.1 osa-miR160b-3p Cleavage 4.5 8.299 1 21
Osa02LNT0178900.1 osa-miR164e Cleavage 5.0 10.387 1 21
Osa02LNT0178900.1 osa-miR408-5p Cleavage 5.0 7.556 1 21
Osa02LNT0178900.1 osa-miR1858a Cleavage 5.0 7.663 1 21
Osa02LNT0178900.1 osa-miR1858b Cleavage 5.0 7.663 1 21
Osa02LNT0178900.1 osa-miR1879 Cleavage 4.0 12.941 1 24
Osa02LNT0178900.1 osa-miR2097-5p Translation 3.5 13.056 1 22
Osa02LNT0178900.1 osa-miR2097-5p Cleavage 5.0 6.96 1 22
Osa02LNT0178900.1 osa-miR5074 Cleavage 5.0 22.794 1 21
Osa02LNT0178900.1 osa-miR5144-3p Cleavage 3.5 16.695 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0178900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0178900.1 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0178900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0178900.1 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0178900.1 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0178900.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0178900.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0178900.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0178900.1 2 qER-2b Physiological trait Eating quality nan nan
Osa02LNT0178900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178900.1 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0178900.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0178900.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0178900.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0178900.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0178900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0178900.1 2 nan Morphological trait Seed C747 C1445
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