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

>Osa02LNT0149400.1

ACACATATAATCTATTTAGAGAACATTATGTTACACAGTACAAAGTAGGATACGAGGAGAGAAAAACGCAGAGAAAACATCTGTTAGTACAATGCCATCCATCAAGATCGTCGTCAATGGAAGCCATGAGATGGCAGCAGTATCAGAAACAGGGAAGCGACGGCGGCGGCCAGCACACGGCAGCCACCGGCGCCGGCGCTGGATCTCGCCGCCGCCGCCGAGCTGCTGCTGTCGGTGGGCTTCGCCGCCGTCGCCGCCTCTTCCGGTGGGCTGGCAATGGCGACAGGCGGCAACGGCGGGTCCAGCACGTCGCCCGGCTCCAGCACCGGCGCCGGCGGCAGCGCCGGCGGCAGCGCCCCCGGCGCTGCCAGGTGCACCAGCGCGCCGGCGTCCGCCGGCAGGATCGCGTAGCTCAGGTTCAGGCTCAGATCGCTGCACGGACTCCGGAAGTAGGTGGCGGCGGTGGCGGGGTACTCGGTGATGAGGCCGTCGGCCATGACGTGGAAGGCGTAGGTGGCGATCTCGATGATGGGGTCGGCCCAGTAGTCGAATCCGAGGTTCATGAACTCGTTCCGGAGCACGCCGACGTAGACGGTGAGGTTGGCGGCGTGCATCCGGTCGGCGACGTCGGTGAACCGCGTGAGGAAGAAGCCGTTCACCTGCGCGATCGACCCGCGGCCGACGGTCACCGCCGTCGCGAACTGCTTGATCTCCTCCACCGACGGCGCCGACGCGTCGCTGATCGTCTCGTCCACCATCAGCACCCGCCTGAACGCCGGGAACTTCTTGAACGCCGCCAGCACCGACGTGTCGTCCGACACCACCATCAGCTCCGGCAGGTGCCCGCCCTCCTTGTCGTAGCTCGCGTTCGCCAGCGCCCCCGACACGGCATCCACCAGCCCGAGGCCTCGCTTCGCGAGGAACGATGCGTGCTCCATCTCGACCATGATGCCAGAGACATTGGTGGCCTTGGCCAAGTCTAGGAATTCAGGCAATGTCACGAACTTGCCGGCGTTCTTCGCGGCGGGGTTCCTCTTCAGGCCTGCCTGGGTGTACGGACCAAGAAGATCGGGTTTTAATGTTTGGATTTCGCTCCATGTGAGATCAAAGGAGAAGATGCCCGACTTGTTCTGAATTTCACTGACAGTGGAGATTTTGGTCATGAAACTGGTGGACGCCGTCGTGCTGGTGCTGAGGTCTGCAGATGGCTGGCAGAAGGCCACGCCGTCTTTCGACATCCGGACCGCGCAATCGATGATGTCGGCGCCGTCTTTCACCGCCTGCTGATATGCGAGGTCAGTGCTGCCCGGGTAGACGCCGCTCGCGCCATTGTGGGTTATGATCAGTGGCCTGCCTCCATCACCACCAGGAGGAGGAAGAGGATTGCCCTTGGTATTTGCCAAACACGCAACAGCTCCTGATGCAGTGGGAGGGAAATCCGTTATCACGCCGTCGACAGAGAAGTTTGCATTGCCAATGTACTGCAAGTACTCTGCACTGGGATCAAAGCTGTAGTTGTAACTCATGGAGACATCATTGGCAAATCCAGAGGCAAAAACTTCAAGCCCAAGGGCATGTGCATCCTTGACCAAACTAGTAGGCAGCCGCAGATACTGGTCCTTGCCCAATGGCCAAATGTATTCCTTGGGGACAAGAATCCCTGATGCAAAGGCCTTGACGGATTTCAGGTCTTTCAGGATCTCTCCATACGTTTTCTTGGTGGTATGCTCAGCGACGTCTTCTCTAAGAAACCGGAAAATTAGCTTGGTGTTGCTTTTCTTGAGCTTAGCACCCACGTTTTTCAAGAATCCAATTTCTGGTGAGGAGATGTAAGCGACACTAAAATCTTTTGGTAATCCTAATATGTAATCTTCGGCACTTAATTTGTGCTCCTGGAGAAATAAAGCATACTCTACATTAACCCATAAATGTGGGGGCTTGAGTCCGACAAGATCTTCAAGGGTAAACATTCCCATGGCTCCATCAAATGTGCTTGGGCGAGAAAAGATGTCCTGGATCAATGTGACATTCTGATACAGCTCGTCTGCGGTGAAATCCAAAGCAAACCACCCATGGATTTCCTCTCCATTCACCTTGTATGTCTTGGCCCTCTTAGGGAAGGCTTCGGCGATAAGCGTCGAGTTCTCTAATGTCAATCCAGTTTTGCAGAAGCCCAAACCATCACTGGACAATTGCAGATCACAGTACAGAACCACATCATGCAAGCTACTCGACATTGCAAACTGGTACGAGAACTGGCTTGAATCAGGAAACAAGCCGGAGAACCCTCCACGAGCAATGACAAGAGGACGCTGACCTCCAAGAGTCTGCCATTTCTGTACTGGATCTTTCAAAGCCGCATGGGCTCCATGAAAAAGTAGGAGGATCAAGAACATGTGAGGATATCTTTCTCCCATTTGGACAGGAGGAGCACCCTCACATGAAACTGCAATAACACAATTGAGAAAAGACGTTCTCCAGCCCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.765624
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0149400.1 2 4848748 T C
Osa02LNT0149400.1 2 4848915 T C
Osa02LNT0149400.1 2 4848992 T C
Osa02LNT0149400.1 2 4849003 A G
Osa02LNT0149400.1 2 4849038 T C
Osa02LNT0149400.1 2 4849066 T C
Osa02LNT0149400.1 2 4849123 T C
Osa02LNT0149400.1 2 4849974 A G
Osa02LNT0149400.1 2 4850541 C G
Osa02LNT0149400.1 2 4851136 G A
Osa02LNT0149400.1 2 4852059 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
Osa02LNT0149400.1 osa-miR5143b Cleavage 2.5 20.764 1 24
Osa02LNT0149400.1 osa-miR5819 Translation 4.5 22.61 1 21
Osa02LNT0149400.1 osa-miR166a-5p Translation 5.0 18.99 1 21
Osa02LNT0149400.1 osa-miR166e-5p Translation 5.0 18.99 1 21
Osa02LNT0149400.1 osa-miR167a-3p Cleavage 5.0 23.628 1 22
Osa02LNT0149400.1 osa-miR166k-5p Translation 4.0 18.99 1 21
Osa02LNT0149400.1 osa-miR166l-5p Translation 3.5 18.99 1 21
Osa02LNT0149400.1 osa-miR390-5p Cleavage 4.5 19.495 1 21
Osa02LNT0149400.1 osa-miR1432-5p Translation 5.0 19.715 1 21
Osa02LNT0149400.1 osa-miR2869 Cleavage 4.5 22.248 1 21
Osa02LNT0149400.1 osa-miR2925 Cleavage 4.5 19.716 1 19
Osa02LNT0149400.1 osa-miR3980a-3p Cleavage 5.0 17.415 1 21
Osa02LNT0149400.1 osa-miR3980b-3p Cleavage 5.0 17.415 1 21
Osa02LNT0149400.1 osa-miR5143a Cleavage 2.5 20.764 1 24
Osa02LNT0149400.1 osa-miR5505 Cleavage 4.5 19.367 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0149400.1 2 qWIJ-2 Morphological trait Seed RM233A RM8
Osa02LNT0149400.1 2 nan Physiological trait Eating quality RM3865 RM3294
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