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

>Osa12LNT0112500.2

ACATATCTATCCCCTATAACTACCCATTGCTTGAGGCAGCAAATGTTACTTCAAACAATGGGGCCTTTCAACAGAAGGCCTCTCCAAACCAAAACAGAGCACACTCAATGAGCCCTCCAGTAACTGGAATGCTCATGAGGTCAAAACAACAGAGCAAGACACAGCTCACCCTCTTTCTAGCATTTTTTGACTTTACCACACTTGTTCCCTCTTCAAGGGGACAAAGGTAAAGAGAACATAAGTATCTACATTGTGCTTCTATCTTTCCTCCATATTTCCTTTGCAGGGAATGTTATGGCAGAGCAAGCTGCGATGCATCAGCCTTCTGTTTTTTTTTCTTTCTTTTTTGGAAAGCAACAGCAAGGGTGAATTGAAGATAGGAGAATGTGAAGTTAATGATAGGATGTACATGATGGATGATGTTTGTCTTGTGGAATAACCCCTGCTATTGTTGCACCAAGTGCTCGCACCATTTATCAGTATCTTTTCTTGGACCAAGTTGCCTCTGATATGCAATGAACTATATGGCATCAACTAGATAGCGGTGGGAAATCACCGTTGTCCTTGAGATGATATGGCTGAGCATTCCTCATTTGATTAGAACTAATTCCAGGATTATGTGCCAGAGACATAGGGCTTGCAGATGCAGAAGGTTGGCTGTCAGAAGCAGTATTCAATCTGTTAATACCAAGCTCTTGGGATGTAACTTCCAAAGGCAATGCTCCCAAGGTCCCAAACTCAAGTTTCTTAGCTGGAGGCTGAATAAAACCATTGCCATGCACAATTTCCCTTGGAGATTCCGAAGATGGAGAAGGTATTGATATGTGCAGTGAAGAGGGGATTCCCAAGTCATTTGCATCAGGATCATAAATATGTCTCAATTCCTCCGAAGGAGTCAAATCTGCTGACATATCAGCTCTACCGTAGTGGTGTGGTCTTTGATGGTTATGTGACAGGAAATGAGTTTTTCCCCTTCCGCCTCGTCCAGAAGGTGACCTGTCTTTGGACAAGTTTGGGTTAGGGAAGTATGTGCCAGTTCCACGAGCTCGATGTGAATCATCTATTTGACTATATGTCCTCATAATTAAATAACCTGGTGGACAAGGAGCAGGGCCTATTCCATTTGTACCAGCATATCCATACACATTATTTCTGCTATGACCATTTGATGATCGCCTATTCTGATATCGTGCAGGTGGTGGGGAAGGCATTTGATAGTACACTGGACCAAATGGATAATATTGGTTCATTGGATAATCTTGGTGGAACCCTTGAGCATAGAGAAGATTATTAAAATTTGTTGTGTAGTCTCCGGTGAGATCTGACCAATTGCTATCAATGGTACCTCTATCATCATTATCCACCTCTTCAAAGGACTGGTGGGATCTGCCTGCGTAACTCACTGTTGACATTCCATGGTGTGATGGGTTTGTGTCATACTTTATGCCAGCCTTCGTACCACTTTCTGACTCATTAAAGAGATCCAGTGCGTCATGACCTTCCTCAGATGGCAAGCTATGTGCTCCGGTAATTGATGGTGATGCAGGCTCACAAGAGTCACTGCCATTCGTCATACCAGTTGAATTAGTAGCTGCAGGATTTGTTGCTTTGCTTGCCAGCCAGCCACCAGAAACAGACTTCCTTTCCTTGTTCTCAGCCACATAATTCCATCCATTTTGCCTTAGCGACCCATGGTTGCTGGAATCTGAAATGCTGATGTTATTGAACTCATCAGATAGATCACCAAAGGAATTATTACTGTATAAAGGCGAACTATCGTTGTCGGCTCTTTCACCATTGAAGTCCAGAGCTATTTCTTGCACATCAGGCCTTACCCTACTGCAGTGTCTCTTCAATGTGTTCCTGAAGAATTGATTCACTTCATCCACAGTAAAATTGTCAGGCACTTGAAGAATCTTCCCAAGCTTCCGGGCACCAAAATCAAATGCACTGCGTATCCGGAGGAAGTTACCTTTGCTGACACTGCGCCCTAGATTGTTACTCTGCTTCAATGGGTCCACTATGTTGAAAAATTTTCGGGGAAAGACCTGAGTATTTTTCTCAGAGTTTCTAGGGAGTACAGTAAACCACTGTGCACATTCCTTGAGAAAGTCCTCTCGCATAGTAAAATCATCATTAACCGTGTCTGGAGAGTCAGTAACTAGCTCAGGCAGGGAAGACAAGGAAATAGGGCCATACAAGCTTATACCCTTATTGTCCCAGTCAAATTTGCTATAGTAGTCCAGAAACCTATAGAGAACAGCTAGTGGACCATCCAATGTTCCATGGAAGAGATGGAAAATATATAACACCAATATCTCCAATGCATAGGTAGAAATTAATCCATGGTGAGCACCAAGAATGCGGCTTTCATAATAACACCAAGCTTTTATCAGCATTATACTTCTCTTGAAAAGGTGGTTTTTTTCAAATTTTTGATCAACCTAGCTTGTGATAAATCAGACCGAGATAGATCTGCAGTTTAAGGAAGAGAACTGGCAACTGCATATTTGTTGCAACTTTTCAAACATTACCTTCTCGAGAAAACAAAGGGTACACAGTCCACCAAACTGATTGAATGAGATGTCTACAATGATGTTTTGAACAATGCATTTCACCAACTTGACCTCTGCATGAATATATTGGACATCCTTGACTTCAAATTCAGCGTCTTTCCTTGCCTCTTCTGATTCTAAAACAGCCTGTACTTGTTTTGCTAAAATTTCATCACTTGAATGGCCAAAGGCAGTCAAATCAATATCTCCATCAGGAAGATAAGTTTTCAACGGAACAGATCCAAATGGAAAGACCTGGCAGCCAACGTTGAACCTGAGGAGGCCCTGGACGTAGGCTATGACGGCGGCGCGGCGGTCCTCGGAGGGCGGGTTGGGCTGGATCCGGGCGACGACGGCTCCGGCGGCGGCCTCGAGGGGATCCCAGGCCTCCTGCGAGATGGATGAGGGGTCGGGGTTGGACGGCGTGGGCACGGGCTCGAGCGCCGGCGAGCAGCCCTGGTTGTCAACCATGGGCGTCGCCGTGGGAGCCCGGTCCAACGCCCCGAGTTGCCTCCTCCCTCCCTCCCTC

Coding Potentia
Explanation CPC Score
noncoding -1.06058
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0112500.2 12 708445 T C
Osa12LNT0112500.2 12 709987 G A
Osa12LNT0112500.2 12 710408 T C
Osa12LNT0112500.2 12 711408 A G
Osa12LNT0112500.2 12 712435 A G
Osa12LNT0112500.2 12 712544 C T
Osa12LNT0112500.2 12 713548 A G
Osa12LNT0112500.2 12 714113 G A
Osa12LNT0112500.2 12 713110 C G
Osa12LNT0112500.2 12 709849 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
Osa12LNT0112500.2 osa-miR5544 Cleavage 4.5 12.352 1 22
Osa12LNT0112500.2 osa-miR5792 Cleavage 4.5 15.549 1 24
Osa12LNT0112500.2 osa-miR5792 Cleavage 5.0 21.163 1 24
Osa12LNT0112500.2 osa-miR5822 Cleavage 4.5 18.226 1 21
Osa12LNT0112500.2 osa-miR5823 Translation 5.0 15.035 1 24
Osa12LNT0112500.2 osa-miR5079b Cleavage 3.0 16.974 1 22
Osa12LNT0112500.2 osa-miR166c-5p Translation 4.5 17.712 1 20
Osa12LNT0112500.2 osa-miR319a-3p Translation 5.0 24.276 1 21
Osa12LNT0112500.2 osa-miR169i-5p.2 Cleavage 5.0 19.714 1 22
Osa12LNT0112500.2 osa-miR166i-5p Cleavage 4.5 15.34 1 21
Osa12LNT0112500.2 osa-miR444a-3p.2 Cleavage 3.0 15.894 1 21
Osa12LNT0112500.2 osa-miR444a-3p.1 Cleavage 5.0 13.622 1 21
Osa12LNT0112500.2 osa-miR818a Cleavage 4.5 18.057 1 22
Osa12LNT0112500.2 osa-miR818b Cleavage 4.5 18.057 1 22
Osa12LNT0112500.2 osa-miR818c Cleavage 4.5 18.057 1 22
Osa12LNT0112500.2 osa-miR818d Cleavage 4.5 18.057 1 22
Osa12LNT0112500.2 osa-miR818e Cleavage 4.5 18.057 1 22
Osa12LNT0112500.2 osa-miR444b.2 Cleavage 4.0 15.894 1 21
Osa12LNT0112500.2 osa-miR444c.2 Cleavage 4.0 15.894 1 21
Osa12LNT0112500.2 osa-miR444d.2 Cleavage 3.0 15.894 1 21
Osa12LNT0112500.2 osa-miR444d.1 Cleavage 5.0 13.622 1 21
Osa12LNT0112500.2 osa-miR444e Cleavage 3.0 15.894 1 21
Osa12LNT0112500.2 osa-miR444f Cleavage 3.5 15.894 1 21
Osa12LNT0112500.2 osa-miR1435 Translation 3.5 21.09 1 20
Osa12LNT0112500.2 osa-miR1849 Translation 3.5 10.13 1 21
Osa12LNT0112500.2 osa-miR2055 Cleavage 4.5 12.308 1 21
Osa12LNT0112500.2 osa-miR5079a Cleavage 3.0 16.974 1 22
Osa12LNT0112500.2 osa-miR5146 Cleavage 5.0 17.968 1 24
Osa12LNT0112500.2 osa-miR2863c Translation 4.5 8.58 1 24
Osa12LNT0112500.2 osa-miR2275c Cleavage 5.0 10.438 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0112500.2 12 gy12 Morphological trait Seed RG869 RG98
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