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

>Osa02LNT0178700.1

ATATTACAAAAAGTGCTTACAGAAAGGGGAAGAATGCCCACTTCAATCTGCTTACAGAAAGGGGAAGGATGCACACTCCAATCTGTTTCAACAAACTAATGGTACAACAATATGGCGAGTAGCTGATTCTCTGGAAAAAAACTGCCATAGCCTCCAAGATGTTGCTCTAAGGGGAAAATCCCCAAAAAATGCTATTTACATTGTATTCCTGCGCCTCTCCATCTGCTATGTGTTAAATTAACACAGGTTAAACTGTTGTCCGTCCAATTGATCTCCCAGTGCCATCAGCACACATGACACTGGTCTATTTTGCATGTGTGCAGCAAGGATGAGTACGCTTCTTACAAAACATTAAACGATCAATACATGGTAAAAATCCAAAAAACAAAATAAGAAAAAAAACTGCATTGTCAGATGCAGAAGCCTGCCACAAGTTAGTCAAAAGAACAGTATTACTGAAATTGTGTGCACAGTTGTTGAACATGTGAAAGATAGGCAGTACCTCAGCGCGTCTCAATAAAGTTGCTAGCACAACAATCCATTCCTTAAATTTGACAGAACACATGTGAGCAACAAGGAACTCAACATCAAGCCGACTTTGAAGAGTATCCATTTGAAGCTGTCATCAGAATATCAATTATAAATGAGAACAGAGATCCAAGGCAGATAATAATATCAGCGAGATTGTGCTAGTATATTGATTGATCAGGTATTGAGTGATTTACTCAAGTAAGCACCATTCTATTTGTTAAACAAACATCCATAATTACTAAGCTTGCCCAGATTCGTAATCTTATATTATGAGCAGTCAATTCAGAACATTATCAAGCTTTGTAAAAGTACAAACTGCAGGAGAAAACTGTAGAAAACTCGAGAAAAATAATCCAAGACCGCAAAGTAGGTGGGAGCTTCTTTGTGCGCTTGTAGTAGCGGACGAGGCGGTGGATCCTGCTCTCAACAAGAATAAGCCTGAAACTTGAGTCCTTGTCCTTCCTGTTCCTCTCCAAATGCTTCCTAATAGCAACAGCCTTCTTGATCAGGAAGTACAGGTCTTCCAGGATCTTCGGTGCAAGACCGTGGGCCTTGAGGATGTGAAGAATCTTGCTACTGGCGATGCTCTTGACGAGGGGGATTCCGTGCTGGTGACGGAGCACAACGCCAATCTGCGACGACATCTGACCCATCTTCGCGGCCTTCATGATCATCTCCTCCACATTGGAGGCGGCGTTCTTGAGCAAGCTCGGGGGAATCCTCTTGCACGGCAGCGCCGACGACGAGATACCCTTCTCATCAATGGGGATAGGATGTAGCCGCAGGAGTTCTGTGGTGGTTGGCACCAGTCATCTCCACGGGCAGCAGCGGCAATTGGAGAGGCGGGGCAACGGCTAGGATGAGAGAGAGGGAGGATCAGGGGAAGAGAGAAAGGAAGAGAAGAAGAGAGGGAGAAGCAGGGGAATAGAGGAAGGAAGGGGATAGGAAGAAGCGGAACCAGGGACAGGCAGCACCGGCCATCTCGGCTGCGGCTGCGGCGGCATGGCAGGGAGTCGAGCATCCAGGAACAATTGGCCAAGGGAATCAGAGAGTAGGAAGTAGAAGAGAAGATTAGGGGTCGCACCCGTAGTGGAGGCCTGGAAACCTTCCTAGAGACCATACCTCGCCGTAGTTTGGCCGGCGGCGGCACCTCGTGTTGAGGAAATCGTGCGTTACCACGGGCTCTTGGCAGTAGCGGCTGCCGGAGGGCGACCGGAGTTGGAATCCAGTAGCCGGCGTGAGGAAGCGCGGTGGCGTTGGCGCCACACCGGCCACGATGCCGCCGGAGAAGGAGGCGGCGTTGACGCGGCCGCCGTGCCGTGCTCCATGCCGGGGAGGCGACGGTGACATCACCACCACTGCACCCCACTCCTTGCCTTCCCTCGCCATCCTTACTTCGCGTGGCCGGCCTCTCCCCGCTAGCTCTGACGGGCGGCAGTGGCGCGGTGCCCGTGTGCGGCCGGATGCGCAGCCGCCACAAGCCCCATTGCCGGCGGGTGGGGTGGGGGGAGAACAAGTGGGGAGGGAGGTGTTGCGGGGAAGGCGGATGATGGTGCCGCACCCGTCGGCCTCCGCCGCTTCGTCGTCCGAAGCTATCGCGGCCATCCTACTCCGTCGTGCCGTCTCCTCCGGCCGCCAGATCCGGCGGCAGCGGAGCTGGATCCAGCCGCGGGAGGGCCGGATCTGACTACGGCGGCACCGGAGACGAGGCCACGAGCCGCGCCGTCGCACGGCCTGCAAGGAGAGGCAACGGATAGCGAGGGGAGGACGGACGACGTCGGCGGCGGCGGGTGGAGGGCGGACGACGACGGAGGTGACTGGGGGAGGGCGGATGGAGGCGGGGGGAGTC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.389797
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0178700.1 2 27671006 A C
Osa02LNT0178700.1 2 27670156 C G
Osa02LNT0178700.1 2 27670393 T G
Osa02LNT0178700.1 2 27668109 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
Osa02LNT0178700.1 osa-miR5804 Translation 3.0 18.564 1 21
Osa02LNT0178700.1 osa-miR164e Translation 5.0 17.531 1 21
Osa02LNT0178700.1 osa-miR5150-5p Cleavage 5.0 12.822 1 24
Osa02LNT0178700.1 osa-miR5500 Translation 5.0 21.145 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0178700.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0178700.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0178700.1 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0178700.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0178700.1 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0178700.1 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0178700.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0178700.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0178700.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0178700.1 2 qER-2b Physiological trait Eating quality nan nan
Osa02LNT0178700.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178700.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0178700.1 2 T2-2tiller Morphological trait Culm/leaf C424 C747
Osa02LNT0178700.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0178700.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
Osa02LNT0178700.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
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