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

>Osa06LNT0349500.1

GATAACGATTTTTGTGGCTTATATTAATACCATTATCACATTAGTGTAAGCCTCTTATAGACAGGATATATACATCCAGTAGATCTGCGATCTGTCGATTCAGGCTAAGCACTCGTTCAGCCAAGCTGGCTACCAAGCTCTATCAAGTTTTTATTCGAGAGATTGATTATCGAGTCGGCGATCACTCGGGCGCTCGACTTCATGTATCCTCCTGATGTTAACATGAGTAGTGGGATGCTTTGATCCTTTGCAAACCTGAACACCTTCTCATCTCTGATCACCACGCCCTGAGGGCTTATCTTCAATCTTCCCAATGGATCGCCATCCAGGATATCTGTCCCAGCATTGTAAACAATCAACTGAGGCTGAAATCTACTTTCTGCAACCTTAAGAGCCTTGTCAAGTTGATCCAAGTAGTCTTCTGTCTTTGTCCCACTAACTAGCTCGACTTTTTGATCAATATACCGCTTAGCAACATGATCCTAAAATGGAGTTGTCAATTTACATAGGAAGTCAGAAAATAGCTGGTATTAGATAAAAGGGAATGATAATGACAAGGACTGGACTTTAAGTTGGTCAAAATTTACATGAAAATCATAGCATTTTTAGATTGAACACCACAACATTTTCGTCTCAAAAAAACAACACCACAACATTTGAATAGAGAGTTTTGTATAAATTGCAGAAATAGACAGTTTGAGTTTCAGTTTTGATATATGTTCAACACTGGTTGTCTAAACCTGATAAAATGCAAAAGTGTGTCCCCTACAGCCTACACAATAAACCCAGAACTTGTATAACCACAAACCCATATACTCCAGATGTTATTCTTACATAGGGATATATTCCAGCATTGTACATATCCAAAGTGTAAACTCTTCCATCATTAGCGAAATCCTTTTCATGGCCATTTCCTTGGTGGGCATCCAGATCTATGATCATCACTCTTGAAATATTTAGACGGACAAAAGCAAACTGAATGCAGAGAGAAATATCAGCATATGCACAAAACCCGCCCCCTTGCTCTGCCGAACAATGGTGAAACCCTCCGCCAACATTAATGGCCCATCCTCTCTCAAGTGCAAGCTTGGCCGATAGAATCGACCCACCCACCTGTTTCCTGAAAGGGTACAGTAGCTTTTGCTGCACAAGCCAATTAGGAATGAATGCCACAGGAGGAAGCTCTACAATGGACGCAACCTTCAGGCTGCTCTTGAGGCTGTTCAAGTACGACTCCGAGTGCACCACCAGCAAATCGTCCTTGGTCGCTTCCAATGGCTCCACCACTCGGTTCTTCTCCAGGTGCCCTTCCTTGGTGAGGAACTTGCATATGCGGCCCCATTTGGAGGAATCGAACGGGTGCAGCTTCTCGATCCCGAGGAAGGCGATGTCGTACGCCGGCGAGTACACCACCGGAGCCTTGGAGCCCGGGACGTCGAGGTAGAGCTTGCTGGAGAGGATGCGGTCGCGGCGGAGGGGGTCCGGCGGGGTCGCCCCCGCCGCCGCGGACGGCGCGGAAGAGGCCATCCACCGGATGCGGGGAGGAGGGGGGAGCTCGGGCGCGGTTGCGGAGGAGGGAGACGAATCGCTGCGCCGCGAGAGGGGCGGCGGAGGACGGCGGCGAGTCTGCCGGCGAGAAGAGGAATGCGCGACCACGTCGCCGGAGCTCGGGAGAATTCGGTGATGTGATATTTGCGATGCACT

Coding Potentia
Explanation CPC Score
noncoding -1.14053
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0349500.1 6 22123439 A G
Osa06LNT0349500.1 6 22123441 A G
Osa06LNT0349500.1 6 22123457 T C
Osa06LNT0349500.1 6 22123595 T G
Osa06LNT0349500.1 6 22125499 T C
Osa06LNT0349500.1 6 22125922 C G
Osa06LNT0349500.1 6 22126053 A G
Osa06LNT0349500.1 6 22126527 G C
Osa06LNT0349500.1 6 22126891 A G
Osa06LNT0349500.1 6 22127002 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
Osa06LNT0349500.1 osa-miR169a Cleavage 4.5 18.771 1 21
Osa06LNT0349500.1 osa-miR169b Cleavage 4.5 18.771 1 21
Osa06LNT0349500.1 osa-miR169c Cleavage 4.5 18.771 1 21
Osa06LNT0349500.1 osa-miR169r-5p Cleavage 4.5 18.771 1 21
Osa06LNT0349500.1 osa-miR1859 Translation 5.0 22.039 1 22
Osa06LNT0349500.1 osa-miR1866-3p Translation 5.0 12.572 1 22
Osa06LNT0349500.1 osa-miR1873 Cleavage 5.0 15.716 1 24
Osa06LNT0349500.1 osa-miR1879 Cleavage 4.5 10.732 1 24
Osa06LNT0349500.1 osa-miR5338 Cleavage 5.0 13.58 1 21
Osa06LNT0349500.1 osa-miR5338 Translation 5.0 15.561 1 21
Osa06LNT0349500.1 osa-miR5489 Translation 4.5 13.57 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0349500.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0349500.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0349500.1 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0349500.1 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0349500.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0349500.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0349500.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0349500.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
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