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

>Osa06LNT0335100.2

CCGGCCAGAAGCCCTCATGACCTCTATCTACTTTCTGTGTCTCGCTATGAGCGATTCTTAGGACGCTTAGAAACAAAATTTGATGCCCACGTTAAAAGGCCCGCGATGCTGACGGCTACTCCAAATCCTGAGTGTAATTCTGCAATTAACTCACGGAGTTCTCTCACGGTACTAGCGAGCAAAGGCTCTCCTGCTGCTCTCTTTCGATTACTAGTCACCCTCTGATTTCCTTGTGGGGCAGAGGTCGTCAGTTGGTGCAGTTGAGCATCGGCTGCATGAACAACGCTCATGGAACTTTGGACGCCCTTCCTCAATTCTTGACTTAGATTACTGAGATCCACAGCCAAGTCACAGATCTCCCTTCCAACTAGTTTCACTGAAGCCATGGTTTCAGGAAGCTTCTCTCTTGCTGAACCGAAGGACTTCTCAAGAGATTCTGCTGCCTTCTTGCATTCCTAAAAATGTCGGCATATCTGTAACGAGGAGGGAGTGGATGGTGCCGTTGATGGTGGTAGGAAGAGCCACCGCCTCTCCTTCTCCCATGCCGCTCGTCGCCGGCCGCCACCGCCGCCGCGTTGGCCGCTGCTGCCCTCGCCCCACCCCGTCCCGCCGCGCCGCGCCGGCTAGCCTGCCCAGGGAAGACCGGAAGAGTGAGAGAGAGGAGTAAGGGATAGAGGAGAGGAAGAAGGGAGAGAAGGTG

Coding Potentia
Explanation CPC Score
noncoding -1.01964
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0335100.2 6 6489770 G A
Osa06LNT0335100.2 6 6489581 C T
Osa06LNT0335100.2 6 6489682 G A
Osa06LNT0335100.2 6 6489912 C T
Osa06LNT0335100.2 6 6490868 A C
Osa06LNT0335100.2 6 6491501 A G
Osa06LNT0335100.2 6 6491796 C T
Osa06LNT0335100.2 6 6491800 A G
Osa06LNT0335100.2 6 6491802 T C
Osa06LNT0335100.2 6 6491815 T C
Osa06LNT0335100.2 6 6491984 A G
Osa06LNT0335100.2 6 6492217 T C
Osa06LNT0335100.2 6 6492275 T C
Osa06LNT0335100.2 6 6492407 T C
Osa06LNT0335100.2 6 6492432 T C
Osa06LNT0335100.2 6 6492492 T C
Osa06LNT0335100.2 6 6492615 A C
Osa06LNT0335100.2 6 6492629 T C
Osa06LNT0335100.2 6 6492691 T C
Osa06LNT0335100.2 6 6492734 C T
Osa06LNT0335100.2 6 6493285 A G
Osa06LNT0335100.2 6 6493691 A G
Osa06LNT0335100.2 6 6491842 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
Osa06LNT0335100.2 osa-miR2096-3p Cleavage 5.0 18.111 1 21
Osa06LNT0335100.2 osa-miR2275d Cleavage 4.5 22.818 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0335100.2 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0335100.2 6 S5 Physiological trait Sterility RG213 C235
Osa06LNT0335100.2 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0335100.2 6 nan Morphological trait Panicle/flower RM276 RM121
Osa06LNT0335100.2 6 nan Physiological trait Source activity RM276 RM121
Osa06LNT0335100.2 6 spf6 Physiological trait Sterility RG213 RM557
Osa06LNT0335100.2 6 qGT-6 Physiological trait Eating quality RM276 RM121
Osa06LNT0335100.2 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0335100.2 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0335100.2 6 nan Physiological trait Eating quality RM276 RM549
Osa06LNT0335100.2 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0335100.2 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0335100.2 6 sd6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0335100.2 6 sd6 Morphological trait Seed RG138 RG64
Osa06LNT0335100.2 6 tns6 Morphological trait Panicle/flower RG138 RG64
Osa06LNT0335100.2 6 tns6 Morphological trait Seed RG138 RG64
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