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

>Osa09LNT0432500.2

GGCAAAATCACACAAAACTAGCTTTATTTATTTATCTCCTTGAAAGGCCAAATCATAAACACCTAGCCATTCAGGAATTAAAATAGTACTGTACAACCCTGGGCGGTAAAAGAAAAAAAGAAAACAGCACAAGAGAAGATATATTTAACCAATGTGCCTATTCAATACAGACAACTGCCCAGAGTCACCGTTGAACAGGTAAACCTCCAATGGTGAATACAACGATGAGAAGGGCGATGACATGAACCTCGTCGATGGCTGTAAGATCCTGCTTCCCTTGGGGCACGGGATGGTCAGAAGACGTGCCCCGGTACGCATTTGCCAGATCTCAATGATGCCTTTCCGTGGAGCATGGATCGCTAGGCACAGGCAATAGTCACTCTTTGTATATTCTGTGTGCAGTGAGCTCGATGCTTTATCTTTGTTCAGAAGCATCTCAACAAAAAGACATGAAGCATCACGGTAACCCTTCCACAGCCGTACAGCCACAAGGGCATGAGTATCCAATAGTAGAATGCGGCCAAGAGAATCAGTTATGGCAGCCAATGTACCACTTGGAGATAGTGTAAGCCGTTCACCCTTCCTCGGTGAATCTTTCAAGCAAGTTAGTGGTGATGTTTTTGCAAAGGACTGAGGCTTAGGACGTGATTTCTTGGTTGGTGATGGTTCGCTCCGCCATATAATTTTAGACAGAGATGATATTGTTGAAAATGTTGCAGCAACACCTCTTGATAAAATTGCTCCAACAATTGACCTGCTTCTGTCTTCTGATAACCTATATGCAGAAACTACAGCATCCTCTCCAACTGTAATTGCACAATAATGGCGCTGACTCGACTGCCCAGCAATATAAAAGCAGCTGAAGTTCCAGCAAGGGAGGTGGCATCAGCCCAACAATTGCAGCATCTGCACAAGAACTGAATTTGCTTACATTCCAAATTTGAAAAGGTATTCTTCCAAAGGAACTATCTTCCTCAGCATCTTCCTGTTCAGATTTGTCTTTCCACAGGTGTGATTTAACTTCATGTAATGATTTTTGAAGCATGTTCTGAAGGTCAGCACCATCAAAACGTGCAATAACACCAGGGAAAACCACAGAAAGCTCATCTGAACCCGAATCTTCCCAGGCGTTTTCCTTCCTCTCACGGAAGTTAAGTTTCAGTATCTTTGAAGGATAAATACTCTGCTTGTGCAGTAGATCGCCTGCGAGAGAGTAGAACAGAAGCCACCCGGCGTCGGTGCCCACGGCGACGGCCACTCCCTCCCCACCAGCCTCCTCGGCGTCCTCCCCGACGAGCGGGACCCACTCCACCGCGGAGATCCGGCCGTCGTCGGGCCCCAGCGCGGGCCTCACCGTGACCCCACCGCCTACTCCGGCGACCGGGACAACCGCGAGCACGGACCTCGCCGCGCTGGCGACGGCGAGGGCGCGCGCGCGCGGCGCGAGGGAGGGGAGCACGGCGGGGTCGTCGAGCCACCCCTCCCTCTCGCCGGCGCCCACGGCGGCGAGGTCCTCGGAGGCCGACGCGAGGAGGGCCACCTCCGCCAGGTGGTGGTGGTGGCCCCGCCGCGCCATGGGGAGGGGAGGAGAGAGGAGGAGAAGCTTCTGGAAGCTTCGAGGCGGGGGCGACGAGATGCCGCCGACGAGGGGTGGAGAGGAGGAGGCTTTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.772838
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0432500.2 9 8713338 G T
Osa09LNT0432500.2 9 8712546 A C
Osa09LNT0432500.2 9 8716776 T A
Osa09LNT0432500.2 9 8710827 A G
Osa09LNT0432500.2 9 8711116 T C
Osa09LNT0432500.2 9 8711321 T C
Osa09LNT0432500.2 9 8711967 A G
Osa09LNT0432500.2 9 8712162 C T
Osa09LNT0432500.2 9 8712419 C A
Osa09LNT0432500.2 9 8712497 C T
Osa09LNT0432500.2 9 8712984 G T
Osa09LNT0432500.2 9 8713198 A G
Osa09LNT0432500.2 9 8713247 A G
Osa09LNT0432500.2 9 8713381 A G
Osa09LNT0432500.2 9 8714676 G A
Osa09LNT0432500.2 9 8714751 A G
Osa09LNT0432500.2 9 8714957 C T
Osa09LNT0432500.2 9 8715417 T C
Osa09LNT0432500.2 9 8715516 A T
Osa09LNT0432500.2 9 8715594 G C
Osa09LNT0432500.2 9 8715717 A G
Osa09LNT0432500.2 9 8715743 G C
Osa09LNT0432500.2 9 8715891 C A
Osa09LNT0432500.2 9 8716620 T G
Osa09LNT0432500.2 9 8710984 A G
Osa09LNT0432500.2 9 8714345 A G
Osa09LNT0432500.2 9 8710490 A 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
Osa09LNT0432500.2 osa-miR167h-3p Cleavage 4.5 11.173 1 21
Osa09LNT0432500.2 osa-miR426 Cleavage 4.5 17.967 1 21
Osa09LNT0432500.2 osa-miR437 Translation 5.0 15.13 1 21
Osa09LNT0432500.2 osa-miR1432-3p Cleavage 5.0 24.738 1 21
Osa09LNT0432500.2 osa-miR396f-5p Cleavage 4.5 17.068 1 22
Osa09LNT0432500.2 osa-miR2930 Cleavage 4.0 22.736 1 22
Osa09LNT0432500.2 osa-miR5338 Cleavage 4.5 20.694 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0432500.2 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0432500.2 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0432500.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0432500.2 9 apd9 Others Others CDO590 G103
Osa09LNT0432500.2 9 nan Morphological trait Root C711 G103
Osa09LNT0432500.2 9 nan Resistance or Tolerance Drought tolerance R1164 R79
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