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

>Osa06LNT0334700.1

CATGTTTCAGAGTTACTCATTTTAAGCTCCATAACTCCGTTGATGAACTTGTTTTACAAGGGGCATTTTACTATACATACAGACAGAACTCCAACAAGGCCTATATATACTATACTTAACAGACAGAACTACAAAACTGTACAAACCACCAGGATGGGTTGGCATCAGGTACAAGCACTAAACAGCTCAGATCAATTGTAAACAGACAGTCACAGATTCCAGATCCCTTGCTTCTCAGTACGGCAGATAGTGAGCATCTCATCATACTTGGAAGCATTGACGAAGCCCCATAGCTCGACATCTTTGACTTCAAACTCCCGGGAACGTGATAAGCACGGGTTGTTAAATGTCTCTGAAGTGGAACTTGAACCATTCAGACTGCAAAGGTAAATGTGTGTGGTTACACACAGGCTTAGGTGGCAGTTAGCACTGCATGCAAACATGGAATGAAAGATATATGCTAAAACTGGAAGTTTTGTGTGAAAAGGTGGCAGGGAAGGATAGACATTACAGGTCTCCATCAAGATAAAGTGCAAAGTGACCACCACCTCCCATTGCCAAATAATCGGTGGAGCAAAATGTGAAATAGTTATTAGCACCTGTTGGACGATATATAACAGGACGGCCAGCTATATTGGTGAACACAAAGCAGTTGTTGGTCCCCTGATACTTCTTTTTTATTAATGGTTGCAATGGGGCCTCAACCAACCCACCGAAAACCGCTCCTTTTCGATCCCCAACTATCAAAAGTGAGTAGCCTGCACAAAGCATGCTCCTTCTATACAGAGTAGATAAAGATATTCCATGTCTCCAGGTACTGTATACCAACATCCAGTTCCTTCCTTGGACAAGTACAGGAAGAGATGTATAAAGAACAGTTCGCATTGTTTCAGACAAAAGCATTGATGGTTCAGACATGGCTGGTAACTTATCATGTGAAGCAGATTCCTTTGATCCCTTAAGTTCCAACCCAGGTGCATCATATTCTGTTTGAACAGTTTCACCATCAATGCTGTAGCTGGGTTTTTGTCTGAAACCACCAATTCTGCCTGCTTTGTTAATGATTTTTCCAATGGAATGCTTCCCTCTGCTAAACAGGCCCTTCCTTCCATTGCTTCCCTTCCCAACAGGTGTTAAAGTTGGATATTCCATATTCATATTGTGCTCAGGTATGATTTCTATAGAATCACTGCTGGAGTTTGATGACGACATAAATGACATCAGGAATGCTCTGAAGGAAGATGTGTCAGGGCCATTAGGAATCTCAGAATTCTTGACTGAATTATCATCATCGTCATCCTCATAGATATTTTCTTGCACTTCAGTGGCCTCGGGGAGGTGGGAGGGGTGGCGCTGGCTCTCCCGCTCGGAGACGGGGTTGAGGATGACGGTGGCGAGGTCGGACACCAGGTGCGCCGCCTTCCCGCCCAGCGACGGCAGGTACCCCATCCCCCGCCTTTGCTCTGCTCTCCGCGACCGCCGGTATGCGTTTTCTCAGGGTTCCCTACCCGACAGCCCAAGCGAGAAGTCCGCGGAACAACATGGGCGAGCTCCTCCGCCGCCGCCGCCGCGGGGACCGAGACCGGAGGAGATGTGGCCAAGTGGGGGCGGCGGAGGCGAGGGGAAGTGGTGAGGCGCGGGAGGTTTGTGCTCCGTGTCGTCGTGTTGGGGCTCGGGGAGGTCAGGAGGGTCAGAAGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.854364
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0334700.1 6 6244235 T C
Osa06LNT0334700.1 6 6243880 C T
Osa06LNT0334700.1 6 6243921 G T
Osa06LNT0334700.1 6 6243940 A G
Osa06LNT0334700.1 6 6244027 A G
Osa06LNT0334700.1 6 6244397 A G
Osa06LNT0334700.1 6 6244554 T C
Osa06LNT0334700.1 6 6244806 A G
Osa06LNT0334700.1 6 6245533 T C
Osa06LNT0334700.1 6 6245715 T G
Osa06LNT0334700.1 6 6246001 A T
Osa06LNT0334700.1 6 6246399 A T
Osa06LNT0334700.1 6 6247027 C T
Osa06LNT0334700.1 6 6247072 A T
Osa06LNT0334700.1 6 6247205 C 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
Osa06LNT0334700.1 osa-miR5802 Translation 4.5 15.839 1 24
Osa06LNT0334700.1 osa-miR1863c Cleavage 5.0 17.878 1 24
Osa06LNT0334700.1 osa-miR5531 Cleavage 4.0 20.179 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0334700.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0334700.1 6 nan Morphological trait Panicle/flower RM276 RM121
Osa06LNT0334700.1 6 nan Physiological trait Source activity RM276 RM121
Osa06LNT0334700.1 6 qGT-6 Physiological trait Eating quality RM276 RM121
Osa06LNT0334700.1 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0334700.1 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0334700.1 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0334700.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334700.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0334700.1 6 AsTol Resistance or Tolerance Other soil stress tolerance RZ516 RG213
Osa06LNT0334700.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0334700.1 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334700.1 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0334700.1 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0334700.1 6 tns6 Morphological trait Seed RG138 RG64
Osa06LNT0334700.1 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