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

>Osa04LNT0250000.1

GAATCGAATTGGGGTTAATTATCTTCAACAAAAGAAAAAACAATACAATTAATACTCAAACCACAAAAAATAGAAAGAAAAGATTACATGAAACAGAAAATTGTTACAGGTAGTATTGTAGCCGAGATGAATGAAAACCTTCTGGCTCTATTAGAGAGAAGGTTTATTCATTGAAGCATGCAAGATAGATAGGTTGCAATTTTGCGCAGTTATTTGGATTAACCACTTGACTAGCAATCCTTGGTACACATGCAGCGGCGCCGGAAGCCGCTGCACTTGCCTCCGGAGAAGCCCTCAGTCAGGCACACGTTGGCGCAGTTGGCCACCATCATGCAGATCCCCTTGAACTCGTTGCTTGGCGTCTCGCACTCCCTTGCCTGTGGTGACAACGAGCAGGAGGAGAACTACAATTGTTGGGAAGAACTTGCGTGATGTCTCCATTTTGATCGATTTGTCTTTGTGTTGATGATCAAATTTGGCACTAGTATTGAATCCCTTGTAACTATGATAATTGAAGTGATTGTGGCGAGGTTTATATATAAAGAGAGCCAATATCATGCAAGTAAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.959339
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0250000.1 4 6053709 T C
Osa04LNT0250000.1 4 6053775 A T
Osa04LNT0250000.1 4 6054223 A T
Osa04LNT0250000.1 4 6054293 A T
Osa04LNT0250000.1 4 6054296 G A
Osa04LNT0250000.1 4 6054321 A T
Osa04LNT0250000.1 4 6054515 T A
Osa04LNT0250000.1 4 6054553 T A
Osa04LNT0250000.1 4 6054594 G C
Osa04LNT0250000.1 4 6054691 G T
Osa04LNT0250000.1 4 6054777 G A
Osa04LNT0250000.1 4 6054809 T G
Osa04LNT0250000.1 4 6054924 A T
Osa04LNT0250000.1 4 6053919 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0250000.1 osa-miR5541 Translation 3.5 18.604 1 21
Osa04LNT0250000.1 osa-miR160a-3p Translation 4.5 23.439 1 21
Osa04LNT0250000.1 osa-miR160b-3p Translation 4.5 23.439 1 21
Osa04LNT0250000.1 osa-miR160d-3p Translation 3.0 23.439 1 21
Osa04LNT0250000.1 osa-miR160e-3p Cleavage 2.5 23.439 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0250000.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0250000.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0250000.1 4 qCTS4-1 Resistance or Tolerance Cold tolerance RM335 RM261
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