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

>Osa06LNT0328200.4

TGGCGGCAAGAAGAGCACATCAAATTAATTGTTCAATATGCACAAAGAAGAGCACATACATCAAATTGATTGTTGATAGAGCCGGTTAGCCGCCTGGTTGTCTCCGGAAAGTTTCAGAAACAAGAAGTACAATTAACGATCCGACTCTGACAGAGAAGTTTCTGAACGAGAGCGAAACCAAATTAAACGATCCAACTACTCTGTGACAAAGTGTTTGATTGCCCAGATCTATATTCTTAGAATTCAATTAAAGAGCACAGCTACAGCCTGGCGATTACATGTGCTGGCATGGGATGCCAAATGGCAAATGATATACCTTCATGTTCGATCCCCGGTGGTCAGTGCTCACTGCTGATGTAGAACAAGTAGCTAGTGAGCTAGCTTTTCCTCATTTTTGACCTTGCGTACCTGCAGCTGGAGTTAAAGGAAACAAGGATCCTTTTAACAGTGATGTACTGCAGTTATGACTTAAGCGTGGCTTCCACTTCCCAGATAACACAAATTGCTGGGTTGAAGTACATAATATATCACAAGTAACCAACTAGGCTGGCGTATTATTGCATGATTAATCAAATATTAACTAATTTTTTAAAAAAATGGATTAATATGATTTTTTAAAAAACTTACGTATAGAAATTTTTTGCAAAAAAACACACTGTTTAGCAATTTGAAAAGTGTGCGCGCGGAAAACGAGAGAGGTGAGTTGGAAAAACTGGGGGAAGAACACAGCCTAAGTTTCTCACTACGAACACATCTATATAAACAATAGTTCTAACTTCATCAACGGCTTAGCATCGCAATGTAAAAACTTATGTTGTTGGGTTGTCAACATCAACAGGTGCTTATTGCTTCACGAGAAATGCAAAATGAGCCAACTTAGGCCTAAGTCTAACCCAGCAAGGTAAACATTATAAACGAACGCTGCGAAGGTCAAATCTGCTCAGACCAAAAGGAGAGAAACAATAGTGCAATGCAGGATGGAGTATATGGATATACGATAAACAAAAGAAATGAGCAAAAACGATGCACTAAAAAGCAAGTGCCGTGTTGGACAGTAAGGATACTCAATCTGCAAGCCGTCAGCGTCAGAAGAAGCTAGCACAGTGCCCTGTAGAGCATCCATAGCAGCCGTAGAGGACTCGATATCCGTAAAATCAGCAAAAGCTACTGGCATTCCACCACGACGGCGCATTTTAAGCAAATGAAATCCAGGTTGCTTAGATAAAACTTCCTTTAGCTCTTCCTCTGTGCATGAGTGACCCAAATTTGCAACAAATAAAGTAGAACAAGGTGGAATATCACTTGACAATTTGTCTGGTTGATCATCTGAAAGAGATTGCCCCCTATGCTGCTTAAGCCCTGGTTGACCACTACTGTGCACGAAAGGAAGCACCAGTCATCAATGACAACCACTAACAATAAGGAAGCACATCAGCAATGTCCTATAGTTTTTACTAGAATGATATGCTAAAGTAAAACATATACATTATATCCAGCTAAGTATGATGTGAAGTGAATTTCAACCTCCGTTCTGCTGGTAATTCATTCTTTTCGTCGGAATCATCATTTTCTGTGTCCAATGGCTCATCAGATCCACCATCTCCATCATTACCACCATTATCATCCTCGCCCCATGCATCATCATCATTACCTCCATCACCAGCATTCTCATGGTCAGCAGCTCTTTCTTTTCTCTTAAGTCGTTTGTCAACAACTCTATAAACCCCACCATCTAGCATGAAATTGCAATTGTGTAAATAGAACGATGTCCAATAACATATTAACATGAGGCAGAGCTAAGTGCACGAAGAATTCTGATAGGAATAAGAAAATTAGTGCTAGTGTCTAAATTACACCTCCATGACGTTTACGTGAACTCGATTTAGCTAGCTCAATGTGCAAACGGTCTCCAGTATCTGGATCAAATACAGTCCCATTTAAAGCAGACATTGCCGAAAGAGCCGCCTGATGATTAACGAATGACACGAAGGCCACCACCTGGTTCCCGCGGCCGGTGTACTCGAGGAGGCAGTGGTCGAAGCCGGGGCGGCTGGAGAAGAGGTTGTGGATCTCCCGGGGCTTCACGTCGTCAGGGAGGCCGGCGACGAAGAGCGTGAGTACCCCCTGCCGCTGCGGATCTGGGTAGGGGTGCGGCGCGTACACGTAGTAGGGGTCTCCCGGCGGCGGGGGGAGGTGGTGGGAGAGGCTCATCTCGTCGGCACAGCGCCGGTGCGGCGGCGGCGGCGGCGGCGGCGCTCTCCCTGCTCCCTTCTCCTGCTCCTACGGCAATAGAGCTCTCGTCCGAACCGAAAATCGGATGAAGAAAAAAGTTAAACAATGATAAATTGAGAAGC

Coding Potentia
Explanation CPC Score
noncoding -1.13338
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0328200.4 6 2636571 C T
Osa06LNT0328200.4 6 2637334 G A
Osa06LNT0328200.4 6 2638060 C T
Osa06LNT0328200.4 6 2639086 T C
Osa06LNT0328200.4 6 2640018 T C
Osa06LNT0328200.4 6 2636532 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
Osa06LNT0328200.4 osa-miR5797 Cleavage 4.0 8.276 1 21
Osa06LNT0328200.4 osa-miR5827 Cleavage 4.5 9.743 1 21
Osa06LNT0328200.4 osa-miR156c-3p Cleavage 4.0 20.76 1 22
Osa06LNT0328200.4 osa-miR156g-3p Cleavage 4.0 20.76 1 22
Osa06LNT0328200.4 osa-miR156k Cleavage 4.0 8.742 1 21
Osa06LNT0328200.4 osa-miR416 Cleavage 5.0 16.759 1 21
Osa06LNT0328200.4 osa-miR1862a Cleavage 4.0 18.76 1 24
Osa06LNT0328200.4 osa-miR1862b Cleavage 4.0 18.76 1 24
Osa06LNT0328200.4 osa-miR1862c Cleavage 4.0 18.76 1 24
Osa06LNT0328200.4 osa-miR2106 Cleavage 4.5 18.212 1 21
Osa06LNT0328200.4 osa-miR5515 Cleavage 4.0 17.575 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0328200.4 6 qAC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0328200.4 6 qGC-6 Physiological trait Eating quality RM190 RM510
Osa06LNT0328200.4 6 nan Resistance or Tolerance Drought tolerance RM170 RM204
Osa06LNT0328200.4 6 nan Morphological trait Shoot/Seedling OSR19 RM225
Osa06LNT0328200.4 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0328200.4 6 qAC-6 Physiological trait Eating quality R2869 R1962
Osa06LNT0328200.4 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0328200.4 6 hr6 Physiological trait Eating quality RM190 RM253
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