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

>Osa06LNT0354000.2

GGAGTAATTCATTGTCCATTACACATCAGAACCACAATAAATTGTGTGGGGTAGTTCGTCTATATTTACAGTCAGCAACACATAGCCACAGGGAAGTGAGCTTACCATGAGTTTTCTGGTGTGTATTCTTTTTTTTTTGAGCTGTTCTTCCCTTGGACTTTGTTGTACAACAATCCTTACTTTTCCTATCACTAACTGACGGACTCATTTCACTCTACAATGCGGATTACTAATCACAAGCAGAAGCTCCAGGGCAGAAGTCAGATCGTGCATATGCCCCTTGCTTTGTCCAAAAACTCGTCCCTGCTTATGCAGCCATTCTCGGTTGGTTTCCACGCATGATATGGCGCCTGAACCTCAGCCCCAACTCTCCTTCCTGATCGCGAGGAATGAGTGCTTGCTCGTGTTCATCATCGTCAGACGCTGTAGTTGTTCCAGGTTCACTTGAATGGAGTGAGTCCTCACCAAAGTTGTGCAGCCTCCGCCCAATCAGATAACGGTCATCCCTAATGGAATTGTGGAGATTGGTGAACCAAACATGGAATCTCTTGCCACAGAAGAACAGCGCGCTGAATATCAGGCAGCCAAGCCACGCGAAACGGTAGACCGCTGAGTTCACAATGAGTGGGTAACCAAGCACTGGGAAGACACCCCTTGCAAGAACATATGGAACGCAGAGAGCTGTAAGGAGCTTGGTGACAATAGGCATTATGATTTCATGCAGGACCCATAGACCTCTCAAACGGGAGAAGCCATCCTCTCTAACCCTCTCAAACTTCGTCCTCCAGCTTTCATCAACCAAAGGTGCCATTTGATCCAACATAACCAGCCTAGTCCATATTTTTAAGAATATTAATCCAAGAGCCCAATCCTGATACAACAGGAAAACCGGACTCTCGTCAATAGGCACCCTCATGGGTACAATGACCAGTAACTCAAACAGGAGTCCAATCAACACAGGAATAACAAAGATCCATATTGACAGGAGAGCAGAACTCTTCACAACAATAGAGCACCACTTGCAGATTTGTTGCACTAGGAAGGCCAGTCGTCGTGATCGAATGTAATCAATTGCATATCTGGTTCCAGCTGCTGCACTCCAGATAATATAACATCCAATGCTGAAAGAGAATAAATCATTGCACTTGATGCCATGTGTGATTGGCAGGCGGGGAATAGCCTCAAAAACTAAACGACCAAGTGAGATTGGAATAACAATCATTCCAGCATTGAATATCAGCAGAGTCATCCATGCCAGTACAAGCAAGAGCACAATCCGAAGGACGAAACCATACTCTGAATCTCCCTGGTCATCAACATCAGATTCTTCAGCGACCTCGTTACTGTCATTGGCATTACCCCTGCCATTCAGATTATCAGCAACATGTTGTATCATACGCTGCTCCAGCTGTGGGGCAACCATTTCCCGGCCACCATGTACCCTATCTCTACCTGCTCTGCCATTCCAGTTCTCTTGCCCACCATTTTCTTCATGTCTTGGCAGTAAGAAATCAGTTAAGCCTAATGCCCAACCAACAGCAGCAAACCAATGACGCAGAAGTGCTTTAATTGTTGCACGAGGCTTGAAGTGCTCAATTGCAAACGGGATGCATATTTGGAACAGAAGCACATCAACTGGGATCTCTGTAAATGGGTCAAAAATGGTGATGTCCAGAGGAAAAATCGATGGAGCTACTCGCATGGCCAGTTTGACAGGTAAGAAAACAAGTATCACAATCAAGCTTCCATACACAGCAACAGACAGAAGAACTCGCCGGGCATGTTTATGCACAGGATCATCAATCAAATCCCTAAACGGATTGTAATTTGGATCGGCAGGGTCCCGCAAGAAATAAAGAACACCATTGCGCAGTACCCCTCGAAGAAGGCTGACAAATATGCTTATTTGAAGCATATATATAATCCCAACAAGCCAATGGATAGAGGAGCTTGCCAAGGGTGACATCGTGAAGAATTCAACTCTTTGAGCAATTGTTGCACCCAGCATCTTTAAGGTGCATACATCAAGCCACCAACCGCACATAAGGGGAAATACACCAAGTTCAATCACCAAAAGGAATGCAACTTTGACCATAGTCATGAGATGCTTCATTCCAGCAAAGAATTGCCTGCATAGAGATGGGATAGCCTCTAAAATGGTAGCTATACCGTAGAGCCTCCCAATGGTGAAACGTTCTCCCCTAGCATACCGCAGTAAAGCCAATGATCCAATGTACAAAAACACAAGGCAAAAGATAAACATATATCCCACAGCAAGAGTTGTCAGATCAGAAAGATAGGATGAGCCAATAGCAGTTCCTTTTATCAGACTACTCTTCCCAGAGGCCTGCATTACAGTAAGACCAGTGGCATTTATCTTCAATGATTGAGTAACCACCTCAATGACATGACCAATGACACCTTCATTATGGCTGTCAGCAGATAAGTTCTTCACGGCATTAAGTGCACTCTTCAATGTATCATTAGCCAATGAAATAGCAGTTTCCGTAAACGGCATCATTCTTGCCAGCATAGGACTAGAGGCTGAAGAGAAGAACCATGATAGATAGTACAGGACAATCCTTCCCAATGAGAATGGTACGAAGATCACAACAATGAGGAATATAGCATTGCTGGCCAGAACCTTCTCGCTGATTCAGTTACCCCATCCGACTCCTCGTCTCCTCCGTCGCTCGCCCCCTCCCACCGCACCGATCCCCAATCTTCGCCGCCCCCCACGATCCTTCTATTTTCCCCGCGGTAGACTGGACGTTGGCGACGGCGGCAACCCAAAGGGCGGCAGCTGCAGCAACGGCAACCTGCAGGGGGGCGGCGAGATTTGTGGCAGCAGCCAGCAACCAGGGTGCGGCGTGACCGGCAATCAGGGGTGGCGGGATTCGTGGCGGCAGCAGCTGGAGCCTCCAAAGCAGGTGGTGAGGTGCAGCTTGCTTGATGGACTCGGTGTACCACACATATTCGCAGTCAACAATGGTGATAGAGGATCGAGAACTGAATCAAATAAATGGGGGCAATTTGGTCTTTTTGACATCACGTTAATTTGGCTACATAACCTTAAAGCGACACATTTTGTGGGACGGAGGAAGTAATATTTATCACTTCCAAATTGGCCCATAAGAAGCAAGAAGTTCTGCAACATGGCAATGTCGTACTGTTCATTAAAAAAACAAGAACATGTTGTGGGGCAGGAAAGCAAAATCCTTACTGTTATTGCGTTCTCAACCAAGTGGAAAACAGGGCCTTGCATGCCTACAAGTTCATCAAAAGGAACATCCTCTGCACCATCTGCATCATCCAAACCATCTAGCATCTGCTCGACTTGAGCTTCAAGTCGTTCTAATCGAGCAGCAACATTTTCTGCATTTCTTCTCAAAAGTTCACCAGCACCAAGTCCTTGGGCTTCTGCTAATTCGTCAACGTTTCCATCTGCAGCAGGAACCCTGTTATTAGGACCAGGTAGCCTTCTGACAGCTCGTGCACCATGCCTTTCACGGCCCCCATCATCCCTCTCAGCATCATGCCCTCCAAGTTCCCGCAAGTGTCTTATATAGTCCCTTAAAGAGGTAGCTCCAAGAAATATAAGGACAATAATAGCTGAGAGAAGAAAACCATGTAAACAGTCACTTAGGATCAACTGAGCGCTGATATGACTCAAGAATAGCCTCTGTGCTTCACCAAGACTTCTCACGAATGTTAACCTCCATATCCAGTAAGTGATGAAGGGGATAATCATGAGCCAAACTGAAAGAACAAAGGCAAGCCGGAGGACAAACTGAAGCACATGGCACGCTTTCATCCCAACACCAACAATAAGTTCTTGGAAGGGGAGTCTTGACGGAGCATTGTCAGCATAGACGGGCGAGAAAGAGAATGCATGTTTGCAAACCTCGCACTGGCGGGAGTTGCTGTGGTCGAGCCACTGGAGGAGGCAGTCCTGGTGCACGAACTTGATGCTGCCGCTGCAGGCGCACGGGTACCGGAGCGGGTGCTCGTCGTCCCCCGGGTTCCGGCAGATCCGGCACACGTCCCCTTCCTCCTCCTCCTCGTCCTCCTCCGCCACCGCCGCGGTGGATGAGGGCGGCCGCGCCTCCTCCTGCTCGGCCGCGGGAGGCCGGTCCGCGGCGACGTCCGCCATGGCTGGGCGCGGCGGCGGCGGCGGCCGTGCGTGCGAGCGATCGC

Coding Potentia
Explanation CPC Score
noncoding -1.16496
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0354000.2 6 25968555 T C
Osa06LNT0354000.2 6 25968807 A G
Osa06LNT0354000.2 6 25969867 T A
Osa06LNT0354000.2 6 25970361 A G
Osa06LNT0354000.2 6 25970472 T A
Osa06LNT0354000.2 6 25972118 A T
Osa06LNT0354000.2 6 25972832 G A
Osa06LNT0354000.2 6 25973230 C T
Osa06LNT0354000.2 6 25972292 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0354000.2 osa-miR5539a Cleavage 5.0 16.664 1 22
Osa06LNT0354000.2 osa-miR5796 Cleavage 5.0 13.8 1 21
Osa06LNT0354000.2 osa-miR5826 Translation 5.0 18.77 1 24
Osa06LNT0354000.2 osa-miR5539b Cleavage 5.0 16.664 1 22
Osa06LNT0354000.2 osa-miR166c-5p Cleavage 4.5 19.882 1 20
Osa06LNT0354000.2 osa-miR395a Cleavage 5.0 15.395 1 21
Osa06LNT0354000.2 osa-miR172c Translation 4.5 16.764 1 21
Osa06LNT0354000.2 osa-miR418 Translation 3.5 13.671 1 21
Osa06LNT0354000.2 osa-miR529b Cleavage 4.5 17.766 1 21
Osa06LNT0354000.2 osa-miR2865 Translation 5.0 19.887 1 22
Osa06LNT0354000.2 osa-miR5076 Translation 5.0 6.679 1 22
Osa06LNT0354000.2 osa-miR5162 Cleavage 4.0 16.076 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0354000.2 6 nan Morphological trait Root RM4447 RM5509
Osa06LNT0354000.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0354000.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0354000.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0354000.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0354000.2 6 qREP-6 Resistance or Tolerance Other soil stress tolerance nan nan
Osa06LNT0354000.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
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