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

>Osa04LNT0249400.1

ATCATTCAAGAAAGCAACTGCTATCGAATAAATTCCAAGAGAATACAAATACAACCGAAATCTATGTCCACGCAAACATTTGGGAAACCACACAATGCTAGTTTATTACAGAAAACAACACAAATGACGATGAACGAAAACGTGGTTTGAAGTTGGAGTTGACGACGAACGATGGGTCTCTTTCACAATCAGTCCCTGAAGAAACCAAAGCTCGAGTTGACGACGGACACGCCGCCGTCGACGCGCAGGTTCTGGCCGCTCACGTACCGCCCGTCGTCGCTGGCGAGGAACAGCGCCGCGGCGGCGATGTCGTCCACCTTGAGTCCAACGCCCTTTAGGTTCGCCGACTTCTCCATGATCGCCTCAATGGTCTCGTCGTCCATGTCCATACCCATGGCAGCCCTAGCCAGCGGCGTGGCGACCGCGGCGGGGGAAACGCAGTTGACGCGGATCCCGTGCCGGCCCAACTCGCCGGCCGCGTTCTCCGTGAACCCCACCAGGGCGCGCTTCGACGTCGTGTACGCGTGCGACGCCGTGCCGGACACCGACGACGACAGGCTCGCCGTCGAGATGATGCTGCCACGGCGCGCCGGCGCCATCACCCGCGCCGCGTGCTTGGTGCCGAGGAACGGGCCGATCAGGTTCACGGCCAGCACGCGCTCGAAGTCCTCCTTGGTGCTCTCGGTGATCCTGAAGCACGGCGGGCCGGTGACGCCGGCGTTGTTGAACATGACGTCGAGCTTCCCGAACGTGGCGACGGCGTGGTCGACCGCGGCGGCGACGTCGCCCTCGTTCGTGACGTCGCAGTGCACGTAGCTGGAGGCGTCCGGGCCGAGCTCCGCGACGAGGCTAGCTCCCAGCTCGTCCTGGATGTCGGCGACCACGACGCGGGCGCCGTGCTTCACGAACAGCCGCGCCGTGCACGCGCCGATGCCGCTCGCGCCGCCGGTGATCACCGCCACCTTGCCCACCAGCTTCCTTGCATCAGCAGAAACATGGGAGCTGCCTGCCATGGCGCCTGAATACTAATAGCAGTAGTGATTTTGGATCGATGTTTTGTGCTGTCTGAGAAGTGGTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.720739
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0249400.1 4 5380241 C A
Osa04LNT0249400.1 4 5380586 G A
Osa04LNT0249400.1 4 5380770 G C
Osa04LNT0249400.1 4 5380959 G C
Osa04LNT0249400.1 4 5381429 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
Osa04LNT0249400.1 osa-miR160f-3p Translation 4.5 16.98 1 21
Osa04LNT0249400.1 osa-miR2100-3p Cleavage 5.0 15.864 1 22
Osa04LNT0249400.1 osa-miR5144-3p Translation 5.0 15.864 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0249400.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
Osa04LNT0249400.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0249400.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
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