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

>Osa02LNT0181900.2

AACGGTAAATTTTGGCATTTATTGGCCGTTTCACCATGTCAATCTGGTATAAGTATCTTGCAGCAGCAAGCAGTGCAGTCATATATTTACACTTTACATTTGAAGGGAGGCAAAGCAATGAAAAACCTGATCATGTATTGACCATATCAACCAAAAAAAGGGTATGAAGAACTATGAATTCCGGCCCATTGCCTCAAACTGTTCTGAAAATGAAAAATGCACAAGGCATTGATGAGATGCATACAGCAGATCAGGAGGCTCGATGGAACATAAATAAGCTGTGCATTGGCTCTTTTAGAATATCCCTTTTGGACTATTATAAGCTGGACTATGTTAAGTGACTTCCAGCACGGTCTTTCTTGACTATCTTCTCAGTTTGCCTCGGGTCACCACTCTGTACTTATTCAGAGTAAGATTTGCTCGGTTTTTTGATAGACCAAAAAAAAAGTGAGAAAAGGGTAACCATGTACAAAGCAATGAAGTTTAGTTTTATGTTGGAATGCCGGCATTAGTAAGTCGTCGACTCTTCTTTTCTTGTTCCTGTACATTGCTGCTAAGTTTATTATGTACAAAATTTTCTTCTCCTAAGATCGGACTCCTTTACAGCTTCCAATGTCTCAGCCATCTGCATTTGTCTAATCACTGTTGCATGCAATACCTGAACAAACAAATTCAAAAACATCACATATAAATAGACGAACAATGAAATACAACAACAAAGGAAGCTAATATTATCAGCTAAACTGCAAAAAGGTAATGAACACATATCCAATGAATTATAACTTCAGTATGCACTACACCCAAGCAAACAACTATATATTAACATGCCCACTCTAGTAGACTCCTAGGATCTGACCCATAGAAGGATTTACGTATGGCAGGTTAGTATAATTGCAAGCCTGCATATTAAGACTGCTATGAACATAACCAATGATAGCGATGTAAGATTTGAAAATGTTATAAAGCACATTTTTAATAAGTACAAAAAACGAATGGCCCTTGGGAGATCTCTTGTTAAAATTTTGGATTTAAATAGGCTGCATTGCATTTTCCTTCTATCTCCAATGTTTAACTTGTAAAGGTTGGACGAGCATAGCCCATGCAGTTCCTATTGGATAGTGTGATCAAAAGTCTCAGGAGTGGATTGGAAGTATCTTAAATCTGCATATTCAAATAAATAAAGCCACAATTTCATAGTTGACTTCAACTATGTTGGTTCAAAATTCTCTTAACTATTTAACAGAAATTCATCTATCAATTACAGAACACCCTTCTGTGGTAAGCACATGACAGAGAGCTAACCTTAAACCTACAAAAAAAAAAGTCAGCACCATAATTCAATTACAGAACACCCTTCTGTGGTAAAACACCATTACCTTCTTTGTCTTCTCCAGATCAAATTCAATGCACTTTATCCTGTCAAAAGAATCCTGTATAGCACGATCCTTATCCTGTGGAATCTCTGGAGGCTTTCTGCTGAGCTGATTAAACATTGTCTCAAGTCTTTCAAGACGCTCTAGACAAGGATTTACACGATCTTCCTTAATTATCTGAAGATCTGCCTGATTACTGTGCACTGTTGTAGTATGCTGGGGGACATTTTCCAACTGTTGTCGATGACGGATGAAAATACGCAAAAAAGAGAGTACTTCAAGAATTACACCGAGAACTTTTTTAGAAATATATTTCAAGATCCCATGATCTGCATTTCCTTCACCATCATTTGGGACGTGACCTGGCTCAGGCGAAACTCTGTTTATTGAGGGATTTTGTCTTGCGCTGTACTGTCCCGATCCATTTCCAGGAGGGTTGTATCTTGTATTCGTCTCAACAACTTTATCATCAGAACCACTGCATGTTGATCCTGACTCCCTGGCCTCCTCATGAACTGGAGCCAAACTATGATACTCAAAATCTTCCTGTCCTATAGGAGATCCAAGATCATCAACATCTGAACCAGATTCAGCATTTGATGTATAACTAATTCTTTCTGGTAACTTGAGAGCACGCAATCTTACAGAGCCTGTAATTGCTTCTTCTATATCAGATACTTGGCCAATGTCCTTCATAATTAAAGGATCACTCCAGGGGCCTTTGTTGGATCGCAGGCATCCTCCCTGGCTAGAGCACGTGCAAGAACCACCAAGAAACTCTGGTAGTTGGCTTGAGTCAATAGCTTCAAGAAGTCTGTGTTGGTATTTTGTTCCTAGAACATGGATTTTAGACGAGGTTTTGGGGTCAAGAAGTCCCTTCACAGTACTCCAGATCAGTTTAAAACCAGGCCCCGCATTTACAATGAACATTTGATGTAGTGTCTCAGGATAATAATCACCATCTATTTTCTGCATACAGCGCACCAAATCCCTTGCGATCTTGCTAAAGTTCTTCCAACCCACACCGTGGACATCCAGTATTGTAGTTGTCGTATCAATATGCTTTTTAGCAGCAATTGAGCATGCAGGAAACTTCTCTCGGAATGCTCTCTCAAATTCCTGTACATGATATTTAATATAGCGTTCCACTGTTGTAATTTGTACAAGCTTACTGGGTTCAACTTTCCCAAGCAACTCGATATAGACGGGCCTTCCTTCCTTGTCAACACCATGATAACCATGGGGATAATACTGCAGCACCTCCTCTAGCTCATGAAATTCAAAATCTTCCAAAATTGTGTCAGTCCCGAAATCCTTCCTCCAGTGCAGCATGTCAGCCCACATATGTGCTGCCTTTTCAACATCAAATTTCCTAGCTTTCAAGAATCTAAGCATCGTGTGATAATCGTCATGCCTCTCAGGCAGCATGTCCCTGGCAAACAAAACCTCTCGAAAAGAGCTGACAGCCTGCTCCTCCTCCGCGTCCCTGACATCCTCTATCGTGATCTTCGGCACTCTGCAGCCCACTTTCCTCTTCCCTCTCTTCTTCAGCGAATGCGTCAGCCTCGTAGATGCATGCAGCGCCTTCTTCTTCAACGACCGTATCCTCGTCTGCCTTGGCTCATCCTCCGAAATCTCAGCGTCCCCTCTGTCCCTCCTCTCATCGTTACTAGCTGATATTTCGATGCCGTCGACATTGCTCTCTGACATTCTCCACAAATGCACCCTCAGACGATCAGACTTCTCACTCTGTATTTTTCTCAAAGATCGCTGATCCGATACTTAGTCACAACCACACGGGCCTAGACGCTCGTCGCCGGGAGAGGAGGAGATCTGCAGCTAGCGGCACGCACGCATCCACCAGCTGCGGCGGCGCGGGACTCCTCCGATCAGGCTCGGATCGGAGAGGCGGGCCAACGGGGGATACCCCCGGCGGCGAGGGAGGATTCGAGGCGGCGAGGGCGAGGGCGAGGGCAACGCGGAGGAAATTCGAGTTCGGTGCGAGCGTTTGTTTTGTTTCGTTTGTTTGATCCGCTCTCTCCTCGCGCTTACGCTTCCAT

Coding Potentia
Explanation CPC Score
noncoding -1.14764
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0181900.2 2 29950800 G T
Osa02LNT0181900.2 2 29951267 A T
Osa02LNT0181900.2 2 29951673 T C
Osa02LNT0181900.2 2 29951693 T C
Osa02LNT0181900.2 2 29953582 A T
Osa02LNT0181900.2 2 29953586 A C
Osa02LNT0181900.2 2 29954327 A C
Osa02LNT0181900.2 2 29954422 C T
Osa02LNT0181900.2 2 29955051 G T
Osa02LNT0181900.2 2 29955985 T C
Osa02LNT0181900.2 2 29955996 T C
Osa02LNT0181900.2 2 29956102 T C
Osa02LNT0181900.2 2 29953976 T C
Osa02LNT0181900.2 2 29956538 T C
Osa02LNT0181900.2 2 29956617 G T
Osa02LNT0181900.2 2 29952999 T C
Osa02LNT0181900.2 2 29953820 T C
Osa02LNT0181900.2 2 29952706 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
Osa02LNT0181900.2 osa-miR5539a Cleavage 5.0 19.035 1 22
Osa02LNT0181900.2 osa-miR5793 Cleavage 4.5 17.118 1 21
Osa02LNT0181900.2 osa-miR5831 Cleavage 3.5 15.696 1 24
Osa02LNT0181900.2 osa-miR6253 Cleavage 3.0 10.124 1 22
Osa02LNT0181900.2 osa-miR5539b Cleavage 5.0 19.035 1 22
Osa02LNT0181900.2 osa-miR397b Cleavage 5.0 13.337 1 21
Osa02LNT0181900.2 osa-miR398a Cleavage 4.5 16.781 1 21
Osa02LNT0181900.2 osa-miR398b Cleavage 5.0 16.781 1 21
Osa02LNT0181900.2 osa-miR529b Translation 4.5 12.234 1 21
Osa02LNT0181900.2 osa-miR444b.2 Cleavage 3.5 18.552 1 21
Osa02LNT0181900.2 osa-miR444b.1 Cleavage 4.5 17.62 1 21
Osa02LNT0181900.2 osa-miR444c.2 Cleavage 3.5 18.552 1 21
Osa02LNT0181900.2 osa-miR444c.1 Cleavage 4.5 17.62 1 21
Osa02LNT0181900.2 osa-miR444f Cleavage 3.5 18.552 1 21
Osa02LNT0181900.2 osa-miR1850.1 Cleavage 4.0 13.96 1 21
Osa02LNT0181900.2 osa-miR1858a Translation 3.5 11.669 1 21
Osa02LNT0181900.2 osa-miR1858a Cleavage 5.0 11.118 1 21
Osa02LNT0181900.2 osa-miR1858b Translation 3.5 11.669 1 21
Osa02LNT0181900.2 osa-miR1858b Cleavage 5.0 11.118 1 21
Osa02LNT0181900.2 osa-miR1846a-5p Cleavage 5.0 17.132 1 21
Osa02LNT0181900.2 osa-miR1846b-5p Cleavage 5.0 17.132 1 21
Osa02LNT0181900.2 osa-miR1846c-5p Cleavage 5.0 17.132 1 21
Osa02LNT0181900.2 osa-miR2100-5p Cleavage 4.0 16.064 1 22
Osa02LNT0181900.2 osa-miR5156 Translation 5.0 15.851 1 24
Osa02LNT0181900.2 osa-miR5156 Translation 4.5 13.721 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0181900.2 2 nan Morphological trait Seed C747 C1445
Osa02LNT0181900.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0181900.2 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0181900.2 2 qLTSPS2 Physiological trait Sterility RM1385 RM240
Osa02LNT0181900.2 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0181900.2 2 qCHR-2 Others Others RM263 RG520
Osa02LNT0181900.2 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0181900.2 2 AsS Resistance or Tolerance Other soil stress tolerance RM318 RM450
Osa02LNT0181900.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0181900.2 2 qDLR2-1 Resistance or Tolerance Other soil stress tolerance RM525 RM406
Osa02LNT0181900.2 2 qER-2a Physiological trait Eating quality nan nan
Osa02LNT0181900.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0181900.2 2 nan Physiological trait Eating quality nan nan
Osa02LNT0181900.2 2 Hd7 Physiological trait Flowering R3393 R2511
Osa02LNT0181900.2 2 qSDW2 Resistance or Tolerance Cold tolerance RM263 RM6
Osa02LNT0181900.2 2 nan Morphological trait Panicle/flower RG139 CDO686
Osa02LNT0181900.2 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