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

>Osa06LNT0352200.2

CACGGCGGCGTCCGTGCCGCCGGCGCCCTCGGGCCGCTCCAGCATCGCCAGGGAGGTGTCGTTCACGGTGGAGAGGAGCATGGTCTTCCCGCCGGACTCCTGCGTGAGCGTGACCAGCTGGGAGTTGTACGAGGCAGGGACGGGGGTGATCCAGTCCGACGCCGCGGTGGCGGCGCCGCCGGTCTTCGCGTCCCAGTCGCCGGTGGTGAGGCCGGCGAGGAGGAACGGCCCGAACAGGATCGCATTCAGAGATGCTACCTGTGGCCGATCGTCATCTTAGATGCATTGGATTTTGGTTTGCAATTTTTTTGCTATCCATGTAACAACCAGTTTTTTTTTCAGCGGTTCAGGTCCCCTATTTTTTTCAATCTAAGCACATGCAAGCCCCTAAGGCTGTGTTTAGATCCAAAGTTTGGATCCAAACTTCAGTCATTTCCCATCACATCAACCTTTTATTGCTTCTGTCCTTAGGTTAATTGGGAACTGGAGTAGCAAGTGATCATCACCACTATCCCACTGCTTGCTGATTGTGAGGAAAGTCCCTGGAGATGCTAATTGCAGATCTTTGTCATTCAGAGTTGCTTTTGCACCATTCATTGATGTCCATGATGGTATTCTCACATTCAGTGTTGCATATTGCCCGTTTGTCTTTGCAGCAGAAATGGAAAGTGAGACTTGAAGATACTGATCTGATGAGCTGAGGGGCTTCACTTGTTGAGTAACAGTAAGACCTGCAGTTCTCCAGTTAAATGTGCTCGGTATGTACTGAATAATGTAGAGCCCTGGCTTGTCTCCTTTCTGCTCAAAGTAGATAGAATCCCCCAGCTTGGAGAATGATTCTATCCCAGTTCCATAACAACACCAAAATGAATTGTACTGTGTTCCCCACCCATGGTAGCTTACTGCTTTAGATCTTCCAGGGCCCTGGGGTAGCATGTAGATCATCACACCAGGATCTCTTCCTCTCTGAATGCTTAGGACACCATTTATCAGTGCTCGCTCGTAGTAATCTGCATACGCAATTTCCTTTGTCCATCTGAATAGGTGGCGAGAAACCTTAAGCATGTTGTAGGTAGTACAGGACTCCTCAGTCTCAGTGGTTAGAGCCTCAGCTAAATGTTTTGGATTTGACCAGAACTCACTGACAGATGTGCCACCAGTGGCATAGCTATGAGAAGAATTAACTATGTCCATGAAGAATGTTGCAATCTCCTTGTAAAGAGGATCACCAGTAACTTCATATCTCATTTGCCCACCGATGACAACAGGAATGTGTGTATTTGCATGAAAACCCGAAAGACTGTCAGCCTGAACTGCAAGCAATCCTAGAAAGCAAGGCTTGTCGAAAAGATGAGCCAGCACCAAATGCCTCTGGTCTTTAGTAATGGTGTACAGCTGGTAGAGGACGTCGTTCATCCCGCCGGTCTCCTCGTTGAGCGACGTCCAGTGCCTCTCGATGGTGTACCTCTGGATGACGCTCCTCACGCGGCCGGCGAAGTAGTCGGCCATGGCGACCACCATGCCGAGCGCCTTGCCGTTCCCGGCCACCGTGTGCTGATCCAGCAGGCCCTGCATGATCTTGTGGATGGTGTAGTAGGGCGCCCAGACGGGGCGGATGGCCTCGAAGCGGTCGAAGAACTCGGCGGGGAAGGCGGAGAGGTAGCCGGTGCCGGCCGCCGCCTGGCAGTCGTGCAGCGCGTCCACCACCGCCGCCATCTTGCCGGCGAGCGTGCCGTTGTGCGTGCTCGCCCACATCTTCGCCGCCGCGCTCAGGTAGTGCCCGACGAAGTGGCCGCGGAGCTCGACGTCGGGGCCCTCCCATCCGCCGTACGGCTTCCCCGGCGCCGGCAGCCCGGCCTGCGTCCTGAAGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.833448
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0352200.2 6 24499604 A T
Osa06LNT0352200.2 6 24496231 T C
Osa06LNT0352200.2 6 24496289 T C
Osa06LNT0352200.2 6 24496304 T C
Osa06LNT0352200.2 6 24496387 A T
Osa06LNT0352200.2 6 24497511 G A
Osa06LNT0352200.2 6 24499842 T A
Osa06LNT0352200.2 6 24500153 A G
Osa06LNT0352200.2 6 24497759 T C
Osa06LNT0352200.2 6 24500094 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0352200.2 osa-miR2873a Translation 3.5 21.191 1 24
Osa06LNT0352200.2 osa-miR5486 Cleavage 4.0 15.821 1 21
Osa06LNT0352200.2 osa-miR5491 Cleavage 4.5 12.013 1 21
Osa06LNT0352200.2 osa-miR6248 Cleavage 5.0 15.206 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0352200.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0352200.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0352200.2 6 qDLR6-2 Resistance or Tolerance Other soil stress tolerance RM1340 RM5957
Osa06LNT0352200.2 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0352200.2 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0352200.2 6 nan Morphological trait Root RM4447 RM5509
Osa06LNT0352200.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0352200.2 6 prt6.1 Resistance or Tolerance Drought tolerance R2549 RG716
Osa06LNT0352200.2 6 qGL-6 Morphological trait Seed R674 R2549
Osa06LNT0352200.2 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0352200.2 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0352200.2 6 nan Physiological trait Eating quality RM253 RM162
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