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

>Osa06LNT0331200.2

TTTAGCACAAAGGCGGACCAAATTATAGGTATAAATTAGCTAGTATGGATGTATGATTTTCTAGCTAAAACATCACCTCATTGTTCCTGAGCCCTTGCAATATAATGATTGCACATGTAATGAACAAACATTCATCTAGTGAACATACACATCTCCAGATTCCTATCAAACAAAATAAAACATATCTCTAGACTCCACATATATAGCATGTGCATTTTTTGGAATCCCATGTCATCAGCTCCAATTGTTTTGGTTATCTAGATACCTACAAACAAAGGACTTCCAGAAAAGATAAACCATTAATAATATTGATTGGCACCATCTGAGAACAAAAAGAGACCATAAATAAGAGTGATAGTATCAAGAACACAGAATAACCCATAAGGTACATATTGAACTTGATGATTTCTCAAGCAGCACTGCTAGTGATAACAATTGAGAAGAGCATGCATCTACTACAGACATCACACCTCTTGATCTGTCTCTACTCTCTAGTGTACCTACTACACATATATAGAATTCTAAAAAAGTAAATACTATCTAAATGCCCAAAATGTAGATAAAAAAGAAAACATGGACTATTCATATCAACAATTTTAGCCATTTACATCTGGTATTGATACTGCCATTTATATTCAGCGCATATCTCGACATATTGCCATTTAGCTTGTTATACATAGAGCCTGACTGACCTAACGAAGACAATATAAATATGTATATTTGTGATCTAGTAAAGTTCTAGCTAATATCAAAATCTTCAACCGAAGTATAGATTTTTTTTTTTGCTAGATGTGCAACATTCCTTGTAATTGTCAGTAAGTTCCATAACCCTTGATTGACACAGTAGTATTGGTTGTTGTGTAAGAAAGATCATATAAAGATGTAGCCTTTTACCATAAAGAAATGATTTGTTGGTACCGAATGCAACATCTTAAAAATGTAATCAATAAGCCTAGGATTGGGAGAATGGACTCAGAATAAGCTTGTTGTCTCATAATGGATATAGAGATGAAGGAACTAAGGCCCCGTTTCTTTTAGCTTAAGATTATTATAATCTAGATTATTGAGTCAGATTACTATAAGCTAGATTGTTATAATATGTAGTAGAATAAGCGGTTAGTTGTTTCTTTCCTAGATTATTAGAACCTAGATTATTAGGTTTGCAAGTCTAAAAAAGGAGTGGGGTGGCATGGTGGGTAATTTTTCACCCAATAATCTGAAAAAAGCTCACCTAAATGAGCTTATCAGATTATAATAAGCTAGGCTCGAGATTATAATAAGCTACTTCAATAAGTTGTCTGTTTCTTTCAGCTTACTCCTAATAATCTGGATTATAATAATCTCAAGCTAAAAGAAACAGGGCCTAAGCTAATAAAAATGGAGATACAAATGCACGAATAACAATACCTTTGAATGGACAAACTGAAAGGTTCAATGCGATATATACCAAGATTGCCAAGTTCGGAGAATCTTTGATGACATATCAATCAATATTCCCAACATAAGATTGTCCAAAAGTATATCATACATACTCTGTCATTCTCTTAGAGAAGACAACAAAGAATTTCCATACGGTCCAAATAGAAGCACAACAATTGGCAAGTGGTGCATATCATGCTGTGTTAGCTGACTGATTCGCAGAAGGGGAAAGATAGTGGATGCGTAGGAAATGGCAACAACAGGCCAGATTAATTACAACATAGATATGTACCACTCCATATGCACTGGAGGAATACCTGCATCTAGAGAGGGATACCTTGGCAACCAACTGCAAGCTAGCAGAGAACAGCTGGGACTTGAATAAATGCATGAAAGTCCCAACTGCAAGCAGAGAACCACATGGGGGCAGCGGCGTTGGTACAGAGGAAGCGATGACGTGAACATGGCCTTTGCAGCGTCGAGCTGGCCATCTGGCTGCGGGAGCACAGGCAAGGGATGCGGGGAGGTCGTCCGGCCGTCGGGGTGGACGCGAGATCGACAGGTGCACGGAGGAGCTGAGGGAGCGCAGGAATGAGCGCGTGCAAGGCGGCGTGTCCCTGGCACCGGAGGACGGACCAAGGGCGACTGGATCAACTGGTGGGGCGTCCTAGACCATCGCTTCCGGCGGCCCCTGAACCAGATCGAGCACCTCACCTAGCGGAGTGGAGAGCGCAAAGGAGAGGGAAGCGGTGGCCGCATGGGGATGAATAGGGATAAGAGGGCGGTGGCGGCTCGCGTTCCTCTCGTCCACGCAGCGACGATGGCTCGAAGAGCGCGGGCTGCGCGGCTGCGCCGGCAGCGGTGGCGGCGGCGACGAACGCGAGGGGAGGAGAAGGGAGAGGCTGCGAAGCGGGCAAGAGGGCTAGGGTTTGG

Coding Potentia
Explanation CPC Score
noncoding -1.34547
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0331200.2 osa-miR5543 Translation 4.5 10.61 1 21
Osa06LNT0331200.2 osa-miR5543 Cleavage 4.5 13.959 1 21
Osa06LNT0331200.2 osa-miR5543 Translation 4.0 10.824 1 21
Osa06LNT0331200.2 osa-miR529a Cleavage 4.5 19.721 1 20
Osa06LNT0331200.2 osa-miR1431 Cleavage 5.0 24.901 1 21
Osa06LNT0331200.2 osa-miR2103 Translation 4.5 22.386 1 22
Osa06LNT0331200.2 osa-miR2876-5p Cleavage 5.0 16.843 1 21
Osa06LNT0331200.2 osa-miR2928 Cleavage 5.0 17.059 1 20
Osa06LNT0331200.2 osa-miR5151 Cleavage 4.0 20.396 1 22
Osa06LNT0331200.2 osa-miR5337a Cleavage 5.0 19.04 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0331200.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0331200.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0331200.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0331200.2 6 nan Morphological trait Panicle/flower RG138 RZ398
Osa06LNT0331200.2 6 nan Physiological trait Source activity RG138 RZ398
Osa06LNT0331200.2 6 nan Morphological trait Seed RG138 RZ398
Osa06LNT0331200.2 6 qNP-6 Morphological trait Culm/leaf RZ450 RZ588
Osa06LNT0331200.2 6 qLW-6 Morphological trait Seed RM217 RM111
Osa06LNT0331200.2 6 qSPTF6 Physiological trait Sterility RM217 RM111
Osa06LNT0331200.2 6 alk6-1 Physiological trait Eating quality RM190 RM253
Osa06LNT0331200.2 6 hr6 Physiological trait Eating quality RM190 RM253
Osa06LNT0331200.2 6 Qbph6 Resistance or Tolerance Insect resistance RM510 RM314
Osa06LNT0331200.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0331200.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0331200.2 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0331200.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0331200.2 6 qRCRJ-6 Physiological trait Source activity RM217 RM402
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