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

>Osa07LNT0391000.2

TTGGCAGTGCTCCTCGAATCACACATTACGGCAAGCATCAACTTTAAGACATCTTTTCAAGTTGTTATTGGTAAATACAGGCACGACGACGCGTTGGTCGTCACACGAACAAAGTCAACCAATCCCCAAGTTAAACGCGACCCAGTTTGGGTCAGGAACCCCTTTTTTTTTTTTTTGCGTCGTCAGTCAGCAGGTGCTCTAAGAAAAACACGAGCAACAGCACCGAGAGGATTTGCCACCGGTGCATGACGGACACTCTGCAAAGCCAGCACCACAGCCATCGCACAGCAACAGCTCCGGAGGACAGTGATGTGGTATCATGCTGCTTTTCTTGTGTCATTTAAGTTTAGATACTCATCAAGTTTAGCAGGAGGCTGTTGGGATGCTGCGCTGCACTGATCGATCCATGTTGACAACACCATCCCTTTGATGCCATGATGCTTCCGCTGGTTGCGACATAGCTCTCTCGCTTTCTATCAGCTTGGGGGTTTCTGATGTTCTCCCAACTCCAAGCAGAGGGTGAGTCGGAGAAGGAGCGACGCAGGAGAGGTGTTGTTCTGTTGGAGAGCCTGAAGAGGACGACGGCATTTCAGTAGCAGCATCTCTGTTCAGATGGCTAGCTTCTGACGGTACAAATACAGTTAGCTCTGGTTGCACCGCTCCCGAGCTGCTGCCGTTCATTTTCTGGCTCCCTGCAGGACCTGGATTTTCGGAATCCCGGATGTGCACAATGATTATCGTAATGTCATCCGTCCTGTTTTCATGCTCCAGCCATAGTTTGTACGACTCTGCAGCAATTGCTGAGCAAGCTTCCCGGGGATCTTCATATGCAGCCACCTGTTGGGATCAGAAAAGGAGGTTCGCAATTAGTGGCATGCAGTCAATAGAGAGAATATCAAGGTCAACCAAGTAATCAAAAGCACATACAATTCAACATGAAATTGTTACTCAAATTTGCATGGTGATGGGTACAAGGCATAAAAACAATAGTTCATTATCACATTACTTTAATAGTAACAAAAGGCAACATACAATCACAAGTAGCCAATCTACACCATTATAATCTAAACCCGCCATGATCAACATCATATATATCTCTTTTCCCTGATTGATAGGGTAATTTATAGGCCTTTGAGAGAAAACATAGTAGTCCCTTCTAGCCTTCTGTTAATAGTATTATAGGCATTTACACAGTTCAAAAAAATAGGATAACATATATTCTGACTGATCCAATACTGAAAAGTCATGCACTTTCTATGTAGATATTCACAGTGCAAGGCAAAAGGTAGAAAACAATGTAAATGAAATAAGCCATGGAAAGCAAAAAAGGCTGTTACCAGCCTGGCTTCCTTACACACGTAGTTGTAGCACATTCATTTAAGGAAAGTGGTGGGAAGGAAAAGAGGTTCATGAGGGGACCGCCCATTATAAACACCACTCCATGTTAGGGCCTAATCAAAACACATTTGACAGCATGCAGGCACATCCGTAGTGAACTAGCAATCAGCAGTCAATTCTAAAGTGACATTTCAGTTTTGAGTCCAATAAGATGTTTCCATCAGCAATACTTTTGGAAAAGTGTTAGATTATTCCTGATTCACACAGCCCATTTTGAGATGTTCTTACAGTGGTTTACCTATCATGCCCCTCGTTTCCGGTCAGACTTCCGATTAGTCAATTTGCTGTTACAAATCAAACGCTAATCCACTATTCTTCTACTACTCAATAGAAAGTACATCCACTTATGCATAACTTTATTCAGAGTGACAGCTTTCATGATGCCAACATCAATCAACCTCAAAACCCAAACCATTTTGTAATCATTACACCTTCCTGCAGTTCCAACTTTTTTGACAAAGCTAAAGGTTGATGGATTATTTTTACATGCATTTATGCAACAACAGATGGAGCAAAAATGTATATCCATGACCAAAATTGGCCTATTCAAATCCACGAGTGCAGCTAGTAGGCTAACTGTAACTTGTTAGCAACCATTAATATCCATCTCACCATAAATCGTGATATCGCATGTACTAAGCTCGCATCCTAACATAACTAGATGACTCCACAGATAACCTCCCCTTCACTGTAATCCGTGAAACGTTGATGATGTTCCGTAATCCACAGGGAATAAACATCACGGTACATAGAGGTTTTGCGCACCCTAGCATGCAACACTATGCTCATCAAAATCCTAATTGGAACTAACATATACCACTTTGTCTTTGTATTGGTGATCTTAACAAAAGCATTAAGCATTAAGCTTACTTCTGTGTCCCACTGGAGCAATTTCATGCTTCCCCTGAACAGAACATATGCCAAAGTCATACTCTGGTTGGGTTTTTGGCTGTGTACATCTAGTTTGGATGTAGAGGCTGGGCTTATCCCATTTTCTAAAAAAAAAAAACCTCTGGTTGGGTTTAAATGTCTCCAGAATGACACACTGGATGAAACCTATTAACTCACACATGCAGAATATAAATCACACTGCAAGGGCTGTTCTAGAATATCTTATACCATTCAAACATTTCATAAGCTTAGCTGCAACACCAGTTCTTGGAACATCGGATGCTTCATATAAGCCAAAGGCTGACAAGTTGACACACTGCATCAAGTTCTCCAGAAAGAAGAAAAGGAAGAAGCAAAAAAATCTTTTACTTCCATTATCAACCATGTTGGCTAGTTAACTATGTGTGGTAGTGATGAATTCATGGTGAGCAGTGCAGTGGAGTAAAAATATTTCAATATTATATCTCGTCTATTCCCAAAATGAAGCTCTGCACCAAGAAGAGTCCAGTTTCCATGAAGCAAATGCACTGGCTAAATACTAATTACTACCTGAGTCACCACTCACCACACCACAGTTCACTGGTATCCTATGTGTGCAAAACAAACATCGAAATGGATTGGTTCAGAAAATATTATGGGCATGAATTAGAGTGGAGAGAGAGGGGGAAATCACCATGTCCACGACATCCTGGCTGGAGAGAAACTCAAACACGCCATCGCTTGCGACGACGAAGAATAGGTGGGCTGGAGTGATCTCTACACTTTTCACCTCAGGTTCGGCGATGACACCAACAGCCTCGGCGGCTTGGTCGCCGAGGCTGCGCGTGAAGGCCGTGCCGGGGTAGAGCCCGTCGCGCGCCCACACGCGAGGTGGGTCCCCCTCGTCGGCGACCCAGCTCTCCGCCTCCGGGTCGCGCACGCCCTCCACCTGCTCGACCGACATCACCCGCGCGCCGCACGCCTTCACGCGGGCGCGCTCGTCGGCGCGGAACGGCGTCTGGTCCCACGAGAGCTCCTCCGCCGCCACGCGCCCCTCGCGCCAAACCCCGGCCACGGCGCGTGAGTCCCCCACGTTGGCCACGTGGAGCGCACCCCCCGCCACCAGCGCCGCCACGGCGGTGGTCCCGCTCATCGAGTCGTCCACCTCGTCCGCCGCGTGCATCTCCGCGTTCGCCGCCGGGAGCGCCTCCCGGAACGCCGCCGCGGGGTCCTCCACCACCACCATCCTCCCCCCTCCCTCCTCCCCCGCCCCCACCCCCACCCCCGCGAGCAGCCGCGGGAGCGCGTCGCGCGCGAACCCGGCGCACGCGGCGCCGCACGCGCCGTGCCCGTCGAACACCGCGAACAGGTGGAGGTCGGGGTGCCCCGCGAACCGCGTCGCCACCAGGTGCGCGTCCTGCGACTCCCTCCCGGGCGAGTCCGGGTACAGCCCCGCCACCGCCAGCGTCGCGTACTCCAGCACCAGCCCCGCCCCCGGCACCGCCACCCGCCCCAGCGTCGCGCCGCCGCGCCCACCCACCGCCCCGCCGCCGCCGCGTCCCCTCTGCCGCCGCGGCACGCAGCACTTCCCCTGCGCGCACCCCATCGCCGGGCTAGGGTTCGCCGAGTGCGCGATTGCTTTTTGGGAGTTTACAAATCGGAAGGGGAATTCGGAAGAGGAGGAGAGAAGAGAGAGAGATCGAATGATTCAAATGGCACTGTGCTTGTGTGAGAAGAAGAAAGGTAAATTAATAAATGCAACGAATAAAATAAAATTTAAACAAAAAAAAAAGGAGGCGTCAAGTGTGGAATTCGT

Coding Potentia
Explanation CPC Score
noncoding -1.02887
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0391000.2 7 26964039 A G
Osa07LNT0391000.2 7 26963810 C A
Osa07LNT0391000.2 7 26964336 A G
Osa07LNT0391000.2 7 26964388 G A
Osa07LNT0391000.2 7 26966363 C T
Osa07LNT0391000.2 7 26967227 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa07LNT0391000.2 osa-miR396a-5p Cleavage 5.0 18.185 1 21
Osa07LNT0391000.2 osa-miR396b-5p Cleavage 5.0 18.185 1 21
Osa07LNT0391000.2 osa-miR396c-5p Cleavage 5.0 18.185 1 21
Osa07LNT0391000.2 osa-miR171f-5p Cleavage 3.5 18.508 1 21
Osa07LNT0391000.2 osa-miR418 Cleavage 3.0 7.616 1 21
Osa07LNT0391000.2 osa-miR169r-3p Translation 5.0 21.296 1 21
Osa07LNT0391000.2 osa-miR1864 Translation 5.0 9.844 1 24
Osa07LNT0391000.2 osa-miR2095-5p Cleavage 4.5 10.247 1 22
Osa07LNT0391000.2 osa-miR2864.2 Translation 3.5 11.731 1 21
Osa07LNT0391000.2 osa-miR2864.2 Translation 5.0 8.163 1 21
Osa07LNT0391000.2 osa-miR1862f Cleavage 3.5 11.325 1 20
Osa07LNT0391000.2 osa-miR1862g Cleavage 3.5 11.325 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0391000.2 7 nan Physiological trait Eating quality R1245 R1789
Osa07LNT0391000.2 7 qPLLN7 Physiological trait Sterility RM234 RM172
Osa07LNT0391000.2 7 nan Resistance or Tolerance Other soil stress tolerance R1245 R1789
Osa07LNT0391000.2 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0391000.2 7 hd7a Physiological trait Flowering RM18 R1789
Osa07LNT0391000.2 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
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