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

>Osa09LNT0427300.1

CACAGATAACGCGGTATCCGGCATCTCCATCATGTTCAATCCATCGCTAATCCTCGCCGCGTTCCCCGCCTCCGCCCTCGCACCCAAATCCCACGGCATTCAATCCATCGCGCAATCTCGCCGCCGCGACAAATCCTCAAAACCGCTGCGCTCACCCCGCCACCGCGCATCCATCCATCCATCGCCATGTCGCGCATCCTCCCCATCCCTCACCGGTGAGAGAGAGGAAGAATGTACACGCCCTCTCTCCCGCATCTCGCGGTCAGCCTCGCGCTCACCACCTGCCCTTGATTGCCATGCCAGTCCGGGCTCCAGCGCCACGGCCGGCTTCTGTCACCAGATCCGCCTCGCCTAAAGCAGCCGACGCCTGATTCTCTCTTGTGCAACTTCCATGCTTGTATGGATCCAGGCAGGCTTTCAGCCGCCAGCGGCGGCCGCTGGATGTGGCTTATCATCTCTGCCCTCGCTGCTGGATCGAGGATGCCGCTCACCACCATAGCCGTTCAAGCAGGGGAAGCTGGTCACTTCTGTGGTAGCACCGAGGGGAATTTTCATGAAGCTCATCCATAGGTGGACGATGGACAGCAATGCCACGGAAGGCGAAAGAGCACGCCGCGACAAGAAAGCTCATGAACCAGCAGATGGACCCTTTTAATCAGACATTGCTTTCTTTTATCAGGTTTTACAGCTTGCTTACACACATACAGTGCTTGCTTTAACAAGTAGTATATGTTTATCGTGTTTAACCTACAGCTTTACAAGTCCAGGTGTTAGATTAGTTGATTCGAAGGTAATCATTTAGTTTCTCAGGGATGGTAATTTGAAGATTGTAAAACCTTCTATATTTAGGCCTATTATATCAGAGTTAATAAAATGGGACTGGAAGAGGGATTTGTGTTCTAATATGAATGTCGACAAGAAGGCAAAACTTTTGGAAAGGAATAATGAGTAGAAAGAAGAGCAACATCTGGTATGAAAGATTTCTGTAACATACACCTAATTTATATGAAACCAACCTGAAACAACAAATTGTGCTTATCAAATTGATAAGAGTACTTGCATTAGCCTATGGCTTGTGTTTTTTTTTTTTGGCTATGAAAAGCTTTGGTATACATTATATTATTTGTATTCTTCCACGGTTTCAGCTTATTTTGGTACCATATTTGAAGGATGGATTAATTCCCCCGAGCACCCCAATTGATGTTGCACAACATAAGCACCAGCTGTTAAACTATGTCACGTAAATGGAGATCTTGGCCTCACTGTCTGCTTGAGTACCCCTACAGGTGAATCCTCTTTCAATATTATATAATCTATCAACAAGTTCAAGTGAATGATTGAGCTATTAGAGGATGGCACATATCTAGCCTTGAGCTTAATCGATATCGTGAGGCAAAGGGGTTCATACAAGTATACACTAGAGGTTCAGTCGATATGATCTTTATATATGCCCGGTGGGTCAATATGTTCTGCTAGGGGCCGCCGTTGACGCGTGGACCGAAAAGGAGTTTTCGGGTTTCAACCGAGTGTACATGAACCTACAGGGTCGCACGCTTAATGGGCCGGAATAAGGGGTTTGGATGGAGATCCAATATGAGCTTAATTCGGATAGGGATCTGAATAGGATTCCTACGGGCCTTGGAGGCCCGAGTGATGGATCCTATATATTCGTGAGGGGTGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.340265
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0427300.1 9 2226439 A G
Osa09LNT0427300.1 9 2227687 A G
Osa09LNT0427300.1 9 2227688 T G
Osa09LNT0427300.1 9 2227755 C T
Osa09LNT0427300.1 9 2226762 C 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
Osa09LNT0427300.1 osa-miR5537 Cleavage 4.5 12.772 1 22
Osa09LNT0427300.1 osa-miR5830 Translation 4.0 6.574 1 24
Osa09LNT0427300.1 osa-miR160a-5p Cleavage 4.0 22.822 1 21
Osa09LNT0427300.1 osa-miR160b-5p Cleavage 4.0 22.822 1 21
Osa09LNT0427300.1 osa-miR160c-5p Cleavage 4.0 22.822 1 21
Osa09LNT0427300.1 osa-miR160d-5p Cleavage 4.0 22.822 1 21
Osa09LNT0427300.1 osa-miR160e-5p Cleavage 4.0 22.822 1 21
Osa09LNT0427300.1 osa-miR5498 Translation 4.0 13.307 1 21
Osa09LNT0427300.1 osa-miR5498 Cleavage 4.5 15.371 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0427300.1 9 nan Morphological trait Root C711 G103
Osa09LNT0427300.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0427300.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
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