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

>Osa09LNT0429500.1

CTCCCCACCGCGCGCTCGCTCTCTCTCGCACCTTCCTTCTCTTGTCGATCAGGTCTCCATCCCCTCCCGTCGATCCCTCCCCCTCCCTTTCCTCCCCCTACATCCGTCCTCCTCCTCGCTCTCCTCTCCGTCTGCATGCACCTCCTCCTCCTCTCGAGGCGGCCACCGTGGCCGGGAGAGGCGAGGAGGTGCCTCGCTGCCGGCGCCAGGGCCGGTGACGGCCGGGAGGGCTTCCTCCTCAACTTCTTCACCCGTTGGCTCCACGGTGGGGCGGAGAGGCCGCTGCGGCCGCGGCTGGAGGAGGTGGGGGAGAGGGGGCGGGAGGTGGCGGGGGAGCTGCCGTGAGCATGCGGCCGAGGGCGCGGCTGTCTCGGCGCGGAGCTGATAAGGTGGGGGAAGTGGATGAGTTGCAGGCGCATGCGCGGTGATTTGGCAATTTGGGGATTTTTGATTTGGATGAACAGATTTTGATTTGGGGATTTGTGAATTGTGTCTTGGATTTTTGATTTGGATGAACATACTTTGATTTTGGGATTTGTGGATCGTATGTTGTGAGTTGTGATTTGGGGATGGGAATTAATTTGCATTTGGGGCAATACTCGGAGGATTTTTTTTCGCTACGCTGGGAGATGCCGAGAGGGAAAGGGAGGAAGAAGGTGCCGACGACGAAGCCGAGGTGGCGTGGCCGCATGGCGGTGGCCGGTGGCGGGAGGCGAATGCAGCATGGGTAGCGGTGGTGGACTGGTGGTGATTCCCAACCGTAGTATTGGAAATAGGAATCGGATGAAAGGAAAGGCTTCCACGCGCGTGAGGTTTGCTGTGACGAAGGCCATCGGTGGATCGGACGCACGGACAAAAAATAATGTGACGAACGAAAAAATACTAACCCTTCTCGCATCACAGGTTAAGTCCTCCTTTGATTCAAAGGAAATTCATATAAATTTTAGAGGATTTTATTTCTATAGGAATTTTTTTGAATCAAAGGAATGGATCTTATGGAATCCTATGAAATTTCTATAGATTGCCTAATGCTATATAATTTTTTGGAGGAATTCTAACATGAGGTAAAATCTCTTGGAAACTTTCTTTTGAGTTTTATCTCCTCTAATTCTTGCGTTTTTCCTGTGATCCAATCAAACGACCATTCCTGTGTTTTTTCTGTGTTTTGCAATTCTCTGTTTTATACTTACATTCCTATCAAAATTCTGCGTTTTTCCTATTCCTATGTTTTCTCGTTCCTGCTATTCAATGAGGCCCTAATTGTTTACTGAAACAAATGGCGTACACAAACAAGAACGAAACATGAACTCCCTCCATCCCACGCAATAGTCAGCCCAGGGGCCTTGGTCTGTCCGTTTGGCCATGGGCCGTACGCTGCTCGGACTCGGGAATTAAATGGTGGCCGACACGG

Coding Potentia
Explanation CPC Score
noncoding -1.0423
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0429500.1 9 4428801 T C
Osa09LNT0429500.1 9 4428853 T C
Osa09LNT0429500.1 9 4428886 T C
Osa09LNT0429500.1 9 4428887 C T
Osa09LNT0429500.1 9 4428889 A G
Osa09LNT0429500.1 9 4428897 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0429500.1 osa-miR390-3p Translation 4.5 22.659 1 20
Osa09LNT0429500.1 osa-miR1858a Cleavage 5.0 3.329 1 21
Osa09LNT0429500.1 osa-miR1858a Translation 4.0 11.483 1 21
Osa09LNT0429500.1 osa-miR1858a Translation 4.5 21.222 1 21
Osa09LNT0429500.1 osa-miR1858b Cleavage 5.0 3.329 1 21
Osa09LNT0429500.1 osa-miR1858b Translation 4.0 11.483 1 21
Osa09LNT0429500.1 osa-miR1858b Translation 4.5 21.222 1 21
Osa09LNT0429500.1 osa-miR2101-5p Translation 5.0 16.802 1 22
Osa09LNT0429500.1 osa-miR5081 Translation 4.5 12.06 1 22
Osa09LNT0429500.1 osa-miR2275c Cleavage 3.5 14.062 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0429500.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0429500.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0429500.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0429500.1 9 Sub-1(t) Resistance or Tolerance Submergency tolerance C1232 RZ698
Osa09LNT0429500.1 9 apd9 Others Others CDO590 G103
Osa09LNT0429500.1 9 nan Morphological trait Root C711 G103
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