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

>Osa06LNT0344000.3

GTCCAAAAGTTCTTGTCCCATGCATCTTCTTCAGTTAGGAGGTCTTGTTTAGGTTTTCTTTCCTCTATCTTCTGTGCTAACAGAAATTAAGGTCTTGCGGAGCTCACTCAGCTGAACCCACTAAAAAAGTAACGAGATCATATACTTTGGGGTTTTACCATGCACCCCAAATACCTTCTGCGTCTGGCACGGTGATATATACACAGGTAAAAATCTGTGTTGGCTACAGCAGAAGGGGGCTAAGGTCTTGTAAGACATCCAGCGTCAGAACCTTGATACCGTGGGAAGCTGGAGTGGTTGCAACGCTGCAATGCGTATAGGCCATCGTAGAATTTCACCTCGTCGGTTAGCTTCTTGTACATCTCATGCCACTCAAGGAGCTCGTTTCGTAAGCGGTCTGCCTTACATAAGAGTTGCTGCTCTGATGCCTCAAGTTTAGAGCACTCATCCTTTAGCACCTTCTTCTGACAGATTAAATGTCTGATCCTTTCATCTTGCATCTGAACAGCATTGACGTCTGGAGGTTGATTAGCGTAATCATTGATGTGCTGCCTTTTTTGAGCCCTCCAATGAATCACTGAGCATGAATTTCTTCTTTTGGATGACTCTCCATTGGAAGACATGTCAAACAATACAGATTCTCTGGCTCTTGAATTGTCATCATAAGCCACTGTGGAAGCTTGAGCTGCTAAACTATCATCACGAGCAACAGTGGATGCATAATGAGCTGGAGGAAGTGCTTTTGTGACTCGAGCATATCCAACTAAATGAGCATGGTGCTTCCAATACTCCAGTGTCATTTCTTTCAACCGTGTCTCAAGTCTATGGAAAAGTCCCGTCTTCTCAAAATCTTGTTTATCATGAGTAGGTCTTATGAAGTTTGCCTCCAAAACCCCAGCAATGCCTTTGCTGTGACTTTTATCAGGGTGAGCACACCAAAAGGGCAGTATAAGGCGGTTCTTGTGGTAGACATTAAATCCATGTATATCCAGTTTTGGAGCACCTCTTAAGTAGCCAATTGTAGTAATAACGTCAACCTCTATGTTTATTCCAACTTGTGGTCGATATTTGATGCATTCACAGTATATGAGATCATTGACAATGTGATGTGGCTCAACAACTTGTCCACACAGGATAACTTTGAAGTGTTTTGGTAGCTGAAGATATAGTATAGATGCATAAACACGAAGTGAATATCGAAAGCGATTTGCGACATGCATATGATTTAGCCTTCCTACTGTCTTCTTTCCATCTGGCATGGCAGGTGCTCCTGAGATCATAATATCCTCTTCATCAGATGCAAAGTCAAGTTCCATTTCCCATGCATCGTTGAACCACAAGTTGAACACAATTAGTTTGGTACCATGGCATCCCATGTCTCCAAATTGATTCAATAAATCATCTTCTGTAGTAAATGGAGACCACTTCAAAAGAGTGGACAAATTGGAAGAAAAATGTTTCTCACCACGGTCCATTATCTTCTTGAGAGTATGAGATGATTCATCAAATTCATAATCAACCACTGGTACTAATATGTCATTGCAGCCAGTTTTTGTAAGGAATGTATAAGAGAGTAGACCAATACTCCGTGTCAATCTCCTATTATCTTGTGTGCAGCTGAATACAATAACATCTGCTCCAAGTCTCATTGTGCTGGTTTTGAACCCATTTCCATATTGTCCAATGGATGAATTCCCACTTTTTTTGGAGAACCCAAAGCTCATGCAATGTCGAAGAGACTCTGGACTCATACCACCTCCATCATCTTGTATTACCAATGAATACTCATCAATGAGAGAACATTTTATCTTATCTATCTTCACAAAGGTTGCTCCATTGTTCACCTTTTCCATGTTAAACATGTAAAACAACAGAATTGAAACACAAATAATGTTGACAGAGTTTAGCATTGATATATTTAAATCAAAACCTCATCAACAGCATTGTCGAGAAGTTCTGCAATAGCACCAAATGCCCACTTGTGTGAAGTAGCATTCGAATGAAGAAACTTGGGGTGAATCCTTAAGTGGTTCTGATCACTGTTGATGGTGGGTTGAGCAGCAACACTGTATTCCCCAGCTTTCCAGAACTGCCGGGGGAATGGCAATGCAATAGACATGGGACGTGAACATAGAAAAGCAGCTGCCTCCCTTGCTCTGACATTGATGAGCATGTGGAAGCTTGACCAGCATTTCCAAACTGCATAGCATCTCTTGAGTGATCACCTTCTGCAACAAATTCCTGAGTTCCAGACTGCATTGTCTCTTCTGCGTCAGCAACTGCTGAAGCAAAGTCCTGATTTCCAGACATCATAACCTCTTCCGTGCAATCACCTGCCACAACAATCCCCTGATCTGCAGATTGCATGGCCTCTCCCTTGCCATCATTTGCTGCAGACAGCTCCTTATTTCCAGATTGCATAGCCTCTTCTGCATCATCAACTACTGCAATGAATCCCTGTTTACACAATGTTACTATGAGGTGAGCTGTTTCACCTTGACCATGAGCTGCAATAAAATTTGGACTGTGTAATGTTGTACACAGAACAGCATCATCTTTGCCAGGAATATTTTGATCTTCCACACCATCTCCTTCAGTGGTCAAGTCAACTAATTCTACATGCATGTCAGCTGCATGAACTTGTCCATGAGGACCAGGTTCTTCTACAATAATCTCCTCATCATCGCACAGGTCAACATAGTCTATTATTGTCATGGTTTAACCTAGAGCAGCAGGCTAAGTTGTCAAGCCGGCGTCCGTCGTCGGAGCACCTGTCAAGCCTGCGTTGGGCGGACTGCGGACGCCGTCGTCGGAGCAGGGGCGGCATCGGGCGGCATGGGCTGGATGAGAGGTGCCGGCGTCGGGCTCCGGGCTGGGAGGAGCAGGTCGGCGCCGGTCGGGGAGGAACAGAGCGGCGTCGGCGGCGCCGGCGTCGGGCGGGGAGTAGCAGGTTCGGCGCCGGCCAGGGACAAGCAGAGGGGAGCGGCGCCGGCGTCGGGCGGAGTCGGCGTCGGACGGGGAGGAGAAGGGGCGGCGTCGGGCGGGGAGGACGGCGCCGGCGTCGTGCGGGGAGGGCGGCCGGCCGGCGCACAAACCCTAGATGCCGCTCCACCCCCAGCGAACGCGAGAGGAGACGGGAAAACGCGAGA

Coding Potentia
Explanation CPC Score
noncoding -1.15524
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0344000.3 6 15923158 C A
Osa06LNT0344000.3 6 15923762 C G
Osa06LNT0344000.3 6 15924065 G A
Osa06LNT0344000.3 6 15924637 T C
Osa06LNT0344000.3 6 15925027 T A
Osa06LNT0344000.3 6 15925265 C A
Osa06LNT0344000.3 6 15925806 G A
Osa06LNT0344000.3 6 15925875 A G
Osa06LNT0344000.3 6 15926412 A G
Osa06LNT0344000.3 6 15926461 T C
Osa06LNT0344000.3 6 15927388 A T
Osa06LNT0344000.3 6 15927473 T A
Osa06LNT0344000.3 6 15929593 G A
Osa06LNT0344000.3 6 15930838 G A
Osa06LNT0344000.3 6 15931077 A G
Osa06LNT0344000.3 6 15932044 A T
Osa06LNT0344000.3 6 15932103 T C
Osa06LNT0344000.3 6 15928559 A G
Osa06LNT0344000.3 6 15927271 A T
Osa06LNT0344000.3 6 15928497 G 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
Osa06LNT0344000.3 osa-miR5801 Cleavage 5.0 13.773 1 24
Osa06LNT0344000.3 osa-miR5512b Translation 4.5 13.535 1 21
Osa06LNT0344000.3 osa-miR6255 Translation 5.0 10.772 1 22
Osa06LNT0344000.3 osa-miR399j Cleavage 5.0 18.346 1 21
Osa06LNT0344000.3 osa-miR171b Cleavage 5.0 15.594 1 21
Osa06LNT0344000.3 osa-miR171c-3p Cleavage 5.0 15.594 1 21
Osa06LNT0344000.3 osa-miR171d-3p Cleavage 5.0 15.594 1 21
Osa06LNT0344000.3 osa-miR171e-3p Cleavage 5.0 15.594 1 21
Osa06LNT0344000.3 osa-miR171f-3p Cleavage 5.0 15.594 1 21
Osa06LNT0344000.3 osa-miR166g-5p Translation 3.0 19.34 1 21
Osa06LNT0344000.3 osa-miR166i-5p Translation 5.0 16.829 1 21
Osa06LNT0344000.3 osa-miR166i-5p Translation 5.0 19.34 1 21
Osa06LNT0344000.3 osa-miR2101-3p Cleavage 4.0 14.875 1 22
Osa06LNT0344000.3 osa-miR2873b Cleavage 4.5 11.432 1 21
Osa06LNT0344000.3 osa-miR5512a Translation 4.5 13.535 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0344000.3 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0344000.3 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0344000.3 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0344000.3 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0344000.3 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0344000.3 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0344000.3 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0344000.3 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0344000.3 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0344000.3 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0344000.3 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0344000.3 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0344000.3 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0344000.3 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0344000.3 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0344000.3 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0344000.3 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0344000.3 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0344000.3 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0344000.3 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0344000.3 6 ph6 Morphological trait Dwarf RZ667 RG653
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