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

>Osa02LNT0179400.1

CCACCCAACCAAACAAGCAAGCATTATTGCATCTGCCATGAGAATTTTACACAAAAATGTCAATTGAAGTACCGAATACATTCAGGTATAATAATGGGAAAACAGCAGAGATAATGTCAGTAATATACTCCAACAACTGCCAACATATGCAGGTGGCATGATGCATCTACTTGAACTGCATACATGACACTTTAACAGCAGTACAGGAACCCTTTAATTTTAACAAAAGATTCCAACAGCTTGATTAAGGGATTTGGGCACAAGGCAGGTAAAGTGCATAAACAACCTTCATTTCCAGGCACTAATGAGAGACTTTCGCAACTTCTCATGAATCATGGCCATCACCAACACCGTCTTTCTCGCTACTTAATGCTGTGCTAGAACCAAAGCATATGGGCGTCGTCAGAGGAGAGCTCCTTTCCTTTGGCCCCAAGCTCACACTTCTCCATGCCATGCTCTGATGCTGCTCCTCCTCCCCATTGTTTAGCCCACCTACTCTTCTGTAGTCCTGTTGCCTCCATTAGCAATTCTTGTCTCCGTTTTCTTTTTTTCCATCCTTTTCTTCTTTTCTTTCTTTCATATCCTGCTCAGTCCTCACCTTCTTGGTTGGATAAACATGCTAACGTGCAGCTAGCTAATGTGTTTTGGACTTTAATTATTATAGTAAGTGATGCTACGGGAGACTGATGAGTGTTTCCTGGAGGAGCACCAAACCACACCAATCGCCATCACATGCACTGCCTTTATATTATTACACTCTTCTGATCCTTCTCATGTGAGCAGTGCAAAGGCCACCACTCCTCCCTTCTCTGGTCTCAACAGCTGCACTTGTCTCTCCAATATTTGCTTCCTATTCCCTCTTCACGCAGCAGGACGCAGTGACTGAGACTGACTCCTCTTGTATGTGTGCAATCTTTAAGAAATAGGAGTGTATCTCTCTGTATGTGTGGGTGAAAACATCATAAGTGAGTGACTGCACACTGCAACAAAGCTGATGAATCAGAGATTCACAGCTACACTCTCTGCGGGTCCCAAGCTCATGTTGCCTCAACTAAGCTAAATGCAAACCCGTGGCTTAGCAAAGTGGCATTATAGACATGACCCTGAAAAGGTTCCGACAGAGATGTGTATATATTTATCCTGCGAGGCATGCATGCCTTGATTGCTTTACTTCTTTGCTCCATAAACCCTGATAATAATTCAGATTTTCACTGTTCCAGGCAGCATTGCTGTCTTATCTTGATCACCACTTTTACTATAGCCATTGAGCAAAGTAAAGCAAGCAACAAACCTCCATGCCTAACAGCATTAACCAACCAAGCTAGAGGGATCTGTAGAGAGAGCATCTGTACCTGATCGGCAGTGGCATTGGCATGTGCATCGGCCCTTCCCTATGCTATGCTGCATCTCCATATCACAAGGTTCCTTCCCCCATCATGCATTGGGTCTCTCTCTCTCTCTCTCTCTCTCGCTAGGCCAGCTCTGACCCCAGATTTGTTTCTACCACGCAGTGCAGCGGCAGCGGCAGCTCCCACACCATTACTCCCCATCGCTGGGGTGCTGATCACGGCGGCGAGGGGAAGAGAGGCGCACGCGGCGACCCGAAACTGGCACGCCGGGATCGGGGAGAACAGCGCCGCCGTCGAGATCGGGGAGGACAGCGCCGCCGTCGACGCCCCTTCGCTCCTGCATCTCCGCACCGGCGGCCTGTACCCGGACTATGGGCTTGCGTGGTTGAAGGAAT

Coding Potentia
Explanation CPC Score
noncoding -1.03421
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0179400.1 2 28176630 A G
Osa02LNT0179400.1 2 28177236 C T
Osa02LNT0179400.1 2 28177377 A G
Osa02LNT0179400.1 2 28178031 C T
Osa02LNT0179400.1 2 28178725 A G
Osa02LNT0179400.1 2 28180244 T C
Osa02LNT0179400.1 2 28180439 T C
Osa02LNT0179400.1 2 28175970 G A
Osa02LNT0179400.1 2 28179980 A G
Osa02LNT0179400.1 2 28175788 A 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
Osa02LNT0179400.1 osa-miR396a-3p Cleavage 5.0 12.206 1 20
Osa02LNT0179400.1 osa-miR396b-3p Cleavage 5.0 12.206 1 20
Osa02LNT0179400.1 osa-miR399d Cleavage 4.5 24.232 1 21
Osa02LNT0179400.1 osa-miR399i Cleavage 4.5 24.232 1 21
Osa02LNT0179400.1 osa-miR399j Cleavage 4.5 24.232 1 21
Osa02LNT0179400.1 osa-miR390-3p Translation 5.0 24.027 1 20
Osa02LNT0179400.1 osa-miR2865 Translation 5.0 22.028 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0179400.1 2 nan Physiological trait Eating quality RG139 RZ58
Osa02LNT0179400.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0179400.1 2 nan Morphological trait Seed C747 C1445
Osa02LNT0179400.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0179400.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0179400.1 2 nan Physiological trait Germination/dormancy RM263 RM221
Osa02LNT0179400.1 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0179400.1 2 qGY-2b Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0179400.1 2 qTGW-2a Resistance or Tolerance Drought tolerance RM526 RM525
Osa02LNT0179400.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0179400.1 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0179400.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0179400.1 2 qER-2b Physiological trait Eating quality nan nan
Osa02LNT0179400.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0179400.1 2 nan Physiological trait Eating quality nan nan
Osa02LNT0179400.1 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0179400.1 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0179400.1 2 oa2.1 Resistance or Tolerance Drought tolerance RM263 R3393
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