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

>Osa02LNT0180900.1

ACCGTAATATGCCTGTACAATTTATTATGCATGATATCTGCTGCAATATCAACCAACCAAGCTGTTCAGTCTCACACTGTCTACAATATAAAGTTATAAAAGCTCAGCTGCGTATAGCATGGAAGCAGCGCTTTACTTCCCAAGCACGGTGAAGAGCCATGAGCAGGGAACAAGTGGTAGCGAATCATACTTTGCAACTTTACAACAATTAATCAGAACATTTGACATTTCTAGATTCTCAAAACAAATCCTATTTTCAATTACCCCTCTCACCAAATCTGAAAAAAGAAAAACAGCCCAATTTGATACACCTTAGCGTCATGCTTGCATCAAGCTTCTCCTCGCAAAGCAGTGTGTGCCTCATGCTGCAACTGTACCTCTCTTCGTGACAGTATATGGGTTGGTCTCGAGCAGATTCTCCAGGGATTTTGCCTTCCTGCTTCTCCCCCGACCAGCCTCCTTGAGTAGCTCTGCAAGCCTCCGCTTTTCGTCATCGACGTCTGGGTTAGCTGTGCCCAGCTTCTCTTCGCGCATCCCAACTACATGTTCCAAGATCTCAATGGCCTCATCCAGCCTTCCCATGGCATCATAAGTTCCAGCAAGATTGCTGTACACTCCTAAAGTATCTGGATGATAAGGTCCATATTCTTGCTCCAGAACAGCTCTAGCTTCCTCAAACAGTTCTGCAGCTTCATTTATCGAGTATCTTTGAACACATGCCAACCCCATCTGGTTCAGGGCAACACCAAAGAAGGCCGTCTTTTTCTCACCACAAGTGCGGAGCTTTGCAATCGCACTCTTGAATGAGTCATAAGCTTCTCCATAGTTCCCCAAAATATAGTGCAAGACGCCCATCTGAGCCTCAATTCCAGCAATTGTGCTCTGTTGACCGGCAGAATTGTTGTACATTTTTAAGGCCTTCTGGAGTAACTTGAGTGCTTGCTCATGCTCATTCATGGTTTCATAAATGGCTGAAACATCAGTTAAACCGGTAGCAATTTCTTCCAATGAAGTTCCTGGAATAGGTTTCTGATAAATTTTAAGGGCATTTTCACAGTATGATTTTGACTCCCTCAGCTTCCCTGTCTTGTTGTATAGATCCGCAAGCCGCACAAAAACAGAGGCCACCGTTGCATGATTCTCCCCTTTGCTAGTCTTGAATACAGTAAGAGCTTTCTGATAAGAAAACACGGCCTCATCATACCGGCCCAAGGAGAGATAAATGTCACCAATGCTGCAATCTACTGATGCTACCTCAGTTTCCTGGCCATTGGCCACCATGGCCATGCTAGCCATCACCAGATGCTCTAAGGCAGCTTCATGATCACCCTTTGTGTCACAGATAAGACCCATCAGCCTCCTATCAGCTGTTTCTTCTAATGAGGCTGGCTCACCATTCTCCCTGTGGATATCAAGAGCCTTCTGGCACAATCTTTGTGCTTCATCAAGTTGTAATGCCTGCACATGAGCTTCAGCCAAGTACCGACAAGTCTCTCCAACTCTTGGATCCTGCTCCCCCAATGTCTGCTTCTGAATTTCAAGCCCTGCGGCATACCATTGCAGTGATAGCGCAGTCTGGCCTAGCATCCCATAGGTGTCCCCCAATTGCATGCACCCAGAGAACTTCGCAAGAGCATGCTCCTGACCTTCTTCAATTACAGGGATCTCAAGGGAGCGCTGTAGTACAGGTACAGCCTCGTCATACTTTCCCAAGTTGCAGTAGATTGCTGCCACAACATGCAAACTCATTACCAAGTTCAAGCTCGGTTTTCCACCAGCACATTTCTCGAATGACTTGGTGGCACGAAGAGCATATTTCAGTGCCCGACGAGGATTATCGGAGGCAATCAAATCTCTCGCATGCTTAAGAAGAAATGGACCAAGGTCTGGATTATTAAGCCCAGCATCTTCAGTCCCATTGTGTGGATTAGGACTAGCTTTCCGTCGACGGCCAACTCGGCTTCCGGGTTTGCTGACCTCGGCCTCACCTTCCTCGGTGGATGCCTTGCCATTAGGACCAACAGAAGACTCAGATTCAAGCTGTGATTTCGCAGCCTTTTTCGACGACTTCTTCGATGAATTCGAAGACATCGCCTTGACGGGAGTCCCATTCTCAGCTGCGGTTACCGCATTAGCGGCATTACCACTCCCTTCCCCTTCCTCCTCCTCAATTACCTTCATGGCCTCCATCTCCCCAGCAACAAGGTGGCGAAGCTCCGAGTCGATCCTCGATTCCTCCCCGTCGGAGCCGAAGCTCTCCCGCGAGGGGGATCCACCCTCGCTTGAGCTCTCCATCTCGCACACATTGTTGTAGAGCTGCTCAATCGATGGCTCCCCGGCGCCGGAACCCTCCACATGCATCTCCAGCGCCTCGCTGTGCATGCTTTTCGAAGCCACCGGCGATCTTGGGGCGGACGAATTGTCCTTGTTCTGCGAGGAGTTCACCTCGTTTTGTGCCTCCTCTGTGACAACTCCATCCACGATAATTCCAGGCATTTTGCGGGAGAATTGTACCAAGATCTTTCAGCTCAAGCCCCCCAATTTCTCCTGGAAACAAACCGCTACTACTATCAGCGAAGCACAAACGCATCGAAAGAAAGAAATCCCGAAGAAACATGGCGGGTCAAATTGGAGGGAAAGAAACCAATCCCCGGATGGATCTCCAATCTACAGCGTGTCCCATCAAGAAATGGCGCGGGAAAGGGAGGGACCACGGATGGAACAACGCGTACCTTCAAGCTCGATCCGAGCCGGAGATGCCGGCCGCGCTCGCGCGCGAGGAGGAGGCCTGCGGCTCAATGGCTCCGGCTTTTCCTCTCGACGCCACGCGCTCTCCTCTCCTCTCGTCTTCCTCTTCCTCTCGATTTGCAGCCGCGAGGAGAGAGAGAGAGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.997874
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0180900.1 2 29287810 A G
Osa02LNT0180900.1 2 29287906 A C
Osa02LNT0180900.1 2 29288570 G A
Osa02LNT0180900.1 2 29288867 T C
Osa02LNT0180900.1 2 29288900 G A
Osa02LNT0180900.1 2 29291258 T C
Osa02LNT0180900.1 2 29289737 A G
Osa02LNT0180900.1 2 29289241 T C
Osa02LNT0180900.1 2 29288825 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
Osa02LNT0180900.1 osa-miR5542 Cleavage 4.0 17.535 1 21
Osa02LNT0180900.1 osa-miR7693-3p Translation 4.5 19.957 1 22
Osa02LNT0180900.1 osa-miR164a Translation 5.0 17.309 1 21
Osa02LNT0180900.1 osa-miR164b Translation 5.0 17.309 1 21
Osa02LNT0180900.1 osa-miR395t Cleavage 5.0 21.914 1 21
Osa02LNT0180900.1 osa-miR395f Cleavage 5.0 15.094 1 21
Osa02LNT0180900.1 osa-miR164d Translation 5.0 17.309 1 21
Osa02LNT0180900.1 osa-miR164f Translation 5.0 17.309 1 21
Osa02LNT0180900.1 osa-miR1425-3p Translation 4.5 23.829 1 21
Osa02LNT0180900.1 osa-miR2106 Cleavage 4.0 18.458 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0180900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180900.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0180900.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0180900.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0180900.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0180900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0180900.1 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0180900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180900.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0180900.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0180900.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0180900.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0180900.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0180900.1 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0180900.1 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0180900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
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