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

>Osa06LNT0348600.1

GGACACACAAGTTTCAGCAGTGTTTCAGTTCAGGCTGCAGTTTCAGCTTCTACTCAAGAACAGCACATATTAACACAATTTCTCCAGGCATTACCAAACATGAATGAGTTTAATCAGAAGGAAGCACAAGAAACATGCCATGTGCCATCAGATATTCACACGAAACATACTAGTCCCAACAAGCAAGTCAGGCTGCTCATTCTACTACTACTAGTTCCTAAGAATGTCACTCTACCCATGATCTTGATAGACAGACGTGGAAGCCAGCAGCTTCGTGGCGCCAGATTCAGGGGCACAATTCTCAACAATCAACGAGCCTATTTCCTCTGCTCGAAACTAAAACCTCCAGAAGCCCATGAGCTTATCCGTTGGATGATAATTTTCTCGGATGGTATGCCACAAGCACTTAGGACATGTAAAACTTGTTGAACCATCTCATCCTCACAGTATTTAATTTCAACTAACTTGAGATGCTTTGACACCAAGAATTTTTCATTCTGATTTTTGTTCGTGCTACCTCTTTTGACCATAGTACGTTGGCTCTTCCGAAGTTGAAGAGTAAGTTTCTCTAGAACCGGTGAGTGTTGGAGGAAGTAAATTAGTGCGCTGGAGTCAGCAGCCATACACCATTCATTGAGCAACAGTGTTTTCAGCTTGTTAAATGTAGGGCAACATCTAAAATCCCTTCTGAAAATGAACTCACCCCAGCGGGACTCGATCGGAGGCGGCCAACCTGCCGCGGCGGCGGCGGCGGCGGCGCAGAAGGCGGTAGCCCTCCCCTTCTCCGTCGGACTCGAGGGTAGCTTCTCGTTAGTGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.974743
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0348600.1 6 21214749 T C
Osa06LNT0348600.1 6 21214861 A G
Osa06LNT0348600.1 6 21215859 C G
Osa06LNT0348600.1 6 21217251 T C
Osa06LNT0348600.1 6 21217772 T A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0348600.1 osa-miR5538 Translation 5.0 14.658 1 22
Osa06LNT0348600.1 osa-miR167d-5p Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167e-5p Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167f Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167g Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167h-5p Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167i-5p Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR167j Translation 4.5 17.842 1 21
Osa06LNT0348600.1 osa-miR2094-3p Cleavage 5.0 19.609 1 22
Osa06LNT0348600.1 osa-miR2863c Translation 3.0 14.138 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0348600.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0348600.1 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0348600.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0348600.1 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0348600.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0348600.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0348600.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0348600.1 6 ph6 Morphological trait Dwarf RZ667 RG653
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