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

>Osa09LNT0430100.2

AGAGAAGTAGAAGTAACCACCGTCCTTTCTATACACGTCTCCATTTCTTTCCTCTCCTTTTCCTTCCCCTCCAAATGCCAACCCAAACTCCACCCAAGCTGCAGCTAATCAAATCATCCATCAACTACTACTATCTCCCGATTAGAAAAAAAAGAAAGAAATCAGGAAGAAATCGCCCATGGCGAAAGAAAAAAGAATTCTTGTAGAGAAAAAAGGGGGACAAAACCCAGAGATGAGAACTACATGGTGGATTGGCTCATGATAGTGCAAATCATTGGCTGAGATGAGGAAAGGCATGTTCATCGACTCCAAGATTGTTCACACCAAATGTCAGGCATCTGAACAAGACAGTCACCCTTAAGAACGAAACAGCTTCTTGCTCAACTCAAACGGGATAGTTCTGGTGGAGAAGGTTCAACCTTAATTATGCAGTATTGCTTCAGAAATCAGAGACTATAGTCTTCACATTGTTTGCTTGTTCATCATTGTAAGCAATTGTTTTACACGGCATCAGCGCCTCCAAGCATGTGGCCACCATCAACAGCCATAGCGTCTGCATAGTTTGCTTGATGCTGGCTCCCAGCATATGGTGCATTCCTTCGCACACGATTGTGCTCATCTGATTTCAACAAAACAGGAAAAGGCTTGTCACATATACATGGCAGAATGTTCATTTGTAATGTTGATATCTCAGTTATCAAGACATTTTTTGCCCTACTAATGCTTATTGCACATGTACGGGATACCATAATTTGTAACCATTTGGCCATAGATGTAAAATGCGGACTGCAAAAAAAACATTGGTGTTGTGGCCGACGATATTTCCGACGAAACGTTCATTGAGTTACAAGGATCCCACCTCCCAGGAAGAAATAAATACAACAAAATATACAAGAAAAGAAGCAATTGGTGTACAACCATGGCAGTTGAAGCTGCTACACCTATTAGGGACTTGGGGGGCAAACTTCCTAAACTAGAAACAGAAATAATTTTTTTCTGCAACATCAGAACGTCCATATCCTTATGTTCAAGGAACAAATAGATTAGTATTTACCAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.97767
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0430100.2 9 5838510 T G
Osa09LNT0430100.2 9 5836448 T C
Osa09LNT0430100.2 9 5837684 A T
Osa09LNT0430100.2 9 5836578 A C
Osa09LNT0430100.2 9 5834390 T A
Osa09LNT0430100.2 9 5834885 A C
Osa09LNT0430100.2 9 5835293 G T
Osa09LNT0430100.2 9 5835580 A G
Osa09LNT0430100.2 9 5837062 T A
Osa09LNT0430100.2 9 5837902 A G
Osa09LNT0430100.2 9 5838359 C G
Osa09LNT0430100.2 9 5838464 A G
Osa09LNT0430100.2 9 5838477 A G
Osa09LNT0430100.2 9 5836688 A T
Osa09LNT0430100.2 9 5834778 A G
Osa09LNT0430100.2 9 5835183 C T
Osa09LNT0430100.2 9 5836494 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0430100.2 osa-miR5536 Cleavage 5.0 16.313 1 22
Osa09LNT0430100.2 osa-miR5836 Cleavage 5.0 14.119 1 21
Osa09LNT0430100.2 osa-miR426 Cleavage 4.0 17.301 1 21
Osa09LNT0430100.2 osa-miR2864.1 Translation 5.0 16.841 1 21
Osa09LNT0430100.2 osa-miR160f-3p Translation 4.5 21.536 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0430100.2 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0430100.2 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0430100.2 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0430100.2 9 Sub-1(t) Resistance or Tolerance Submergency tolerance C1232 RZ698
Osa09LNT0430100.2 9 apd9 Others Others CDO590 G103
Osa09LNT0430100.2 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