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

>Osa06LNT0350100.1

GCTAGATTCATGTTGGCCTCTCCAACACCCAAGTCACAAGTAATTAATAACATTACTGTCCACATATATATAAATCGGACCAAGTTTACATATATGGCATATAAATCACGGGAGTTTCCTCATCTTGGACGAAGTGGATAGGCCGGCGCTTCCATATCCCTCTTCCACGGTTTCTACCAGACGCGACGTGGGAAGTGGAAGGTCACCTTTTGTCTTCATCAGTGACGGAGCTAGAAAATCTTCACATCAAGTGCTGAACTGATAGGAGTTTAAATATTTCCATAAATTACATGGTATTTTTAAGATTATAACGAGCAATTAAGGATTATGGAACCAGGCATAAGGTCAGTGGCGGATCCATAGTGTAAGCATTGATTTCAGCTGACACCAATAACTTCTCGCTAATCTCTTTGCTAATACACTCTAGAAACAAGAATTATATGTATTGACATCACTATATTTGAGTAGTGACCTCAATGACTCTATTTTCTGGATCCGCCGCTGCATAAGGCTGAAGGCCTACTGCCCCATAATTGTTTCCGCCCCTGGTCGACGACGCCGGCTACGTCTTTATTCTCTGTCCCAACCGCGCAGAGGCGGGGTTGGGATTGTCATGGGGGACCTGGGGGACCTGGGGGAGGATGTCGAGGATCAGGAGGGTTGTGAATCGGGTCAATAGTAGGCGTGTGTGGAATACCCCGTGGAGCACGATCACTGTCATGGGATGGTGCAGCCGGAGGAGGAGGAGGATTGTTGATGGCAGCGGCGGCAGGACAGCTGACGGCGGCAACTGGAGGCTGAGCTGCCGATGGAGAGCCGCAATCACTAGCAGCGGCTGGATGCTCAGTGTCCCGACGAGCAGGCGGCGGATCGCCGCCGGCGCCGCAGCCGTTAATAAGTGACATTACGGTCTGTTGCTCTGGGTGAGTGACGGCTGATGAGTGGCTAGCTGAGTTATAGATGGAACTTTGCCGTATCAGACGAGTCAGTTGTCAACGCGGCTAGACAAGTCTCCTCCTAGCCGCGGAAGCCCTAGTTGCCGCGACGGCCCGCTTCCTTCCCAATCCCAAGCGCCGCCCGCCTTCTGCCGCCGCTTGGACCTCGGCAACCCCAGCACTCGGCTGGCACTGCGCCGGTAACCGGTCGCCGCGCTTTCACCATGGGCGGCGATTCGCCGACGAGCCATGGCGATTGCCGTTGTCGCCGGCGGGGTGCGCGGGTGGGTGGATGGGCGGACCAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.201065
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0350100.1 6 23018549 A C
Osa06LNT0350100.1 6 23018596 A G
Osa06LNT0350100.1 6 23018947 C T
Osa06LNT0350100.1 6 23018981 C T
Osa06LNT0350100.1 6 23019855 A T
Osa06LNT0350100.1 6 23020606 G A
Osa06LNT0350100.1 6 23021031 A G
Osa06LNT0350100.1 6 23021094 G A
Osa06LNT0350100.1 6 23021181 C T
Osa06LNT0350100.1 6 23021238 A T
Osa06LNT0350100.1 6 23021312 T 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
Osa06LNT0350100.1 osa-miR162a Cleavage 4.5 22.335 1 21
Osa06LNT0350100.1 osa-miR169f.2 Cleavage 4.0 24.196 1 21
Osa06LNT0350100.1 osa-miR1865-5p Translation 3.0 24.381 1 24
Osa06LNT0350100.1 osa-miR2092-5p Cleavage 3.5 16.643 1 21
Osa06LNT0350100.1 osa-miR5151 Translation 5.0 18.065 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0350100.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0350100.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0350100.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0350100.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0350100.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0350100.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0350100.1 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0350100.1 6 RPLD4 Physiological trait Eating quality RG424 RG172
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