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

>Osa04LNT0257000.1

AAATTATTTTTTTCCTTAATATGCTGTACGGCATATTATCAGAGTATATTCAAAAGATGGGGGCCTGATATCATTCCTAGAACCTCCCAAAAGCACATTCAGCCATAGTATTTTCTCACCAGTCACCACATCATTACATTACATTACACTACACACTCGGGTACATTGTGTAGCGTACAATGTTTCCTTTTCAGTTCTCTCGAGTGGTCAGAGAACACCATCTAAACACCCCTACCCTTTTTCCCTCTTTGGTGAAAAGAATTTAAATCAAATGAATTTCCACTAGAGTCCGTGTCATACACCGGAGTTAGAATATTAGATAGCTGTACACCATTGTTACCAGCAACACAGCCAAATGCTTCTGCCAATGAAACCTCCATCCTGAGGAGATGTTGTGAGCGTCAACAGTGTATGTTGCCCCTGTCTGTTCATCCTTAATTTTAATGCTAGAGGAACAGTTGTACTCAGTCCAGCCAATGACTTGATTTTCCAGGTCATAGACAACTAACTTATTTGAAAGGACCAGATCTGGAAAAAAAACAGGTAATAGCACGAACATCATATATATAACAGTTCTAAAAAAACATCAGATATATAACATTGAGTAAAGGATTTGCATGTGCTGAGCAAGACAAACCTCCCAAAAGCACCATACCCTTCCCATCCTTTGATTGTAATCCACCATTTTGGAATCCAACACAATATAAGTTATCCTGCTTAAATACAAAAAAAAAAATCACAAATCTAAGTGTCATGAACATATATCTGTGAACCTGCATATTATGATGTTATATACAGAACATAACAACTACTACAAGACTGAATGCAACGGTATAGTATCATTTCAAACTATAGTACTCCATTAAATTCAAATTAACTATCATGATCGTTGATTGGAACAATTAG

Coding Potentia
Explanation CPC Score
noncoding -1.36633
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0257000.1 osa-miR398a Translation 5.0 12.829 1 21
Osa04LNT0257000.1 osa-miR167d-3p Cleavage 4.0 12.414 1 22
Osa04LNT0257000.1 osa-miR418 Cleavage 3.5 3.733 1 21
Osa04LNT0257000.1 osa-miR2055 Cleavage 3.5 18.02 1 21
Osa04LNT0257000.1 osa-miR5147 Translation 4.0 18.459 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0257000.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0257000.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0257000.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0257000.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0257000.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0257000.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0257000.1 4 nan Morphological trait Root RZ69 RG449
Osa04LNT0257000.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
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