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

>Osa04LNT0253500.1

GAGGCATGATCTAGCATATTACTCTTACTCTTGCTACTGCAAAGTATTAGAATATAGATGAAAACAAAAACTTATCTTGTTTAACCCGGGTAAAGTTAGCGGTCCGCATATGCATCTGCATAGCGTATACCAGCACTGGCAGGATGACGGGCTCGTGGAAGATCTCCATATGCGTGTATGCAGATCGGATCGCACACATATACATGTGTGCTAGTCTGATTTGATGGAGATCAGTACGTACACGCTGGTCGGCCTCGTGCGGCTTGCACGTGTAGTTTGCGATCGAGCAGCCTGGTCACAACATCTCCGTGCGTGGGCGTGCGGCGCGCGGTTGCCGGCACGAGAGACGTGTGGACGCCTGGTGGCGGTGCCTCGCACGATGCAGGAGGAAAATCGACCGATGGCGTACATGCAAAACGATAGATCAATCGTGGTTAGATACGTATCGATACATATGCAAACGCATTAGTGAATTGAAATTGGATAGGTCCATATGGCTGCTGCAGCTGCAATCTGCGCATGTGCATGCGCATGTGTCAGCGGCTTGGGGGCTCCAGTGAGGACGCCGGCGGGTTTGCTGCTCCGGGCTGCCGCGGTGCGCGGCTACATGCGGAGGCGATCGTCTCGGCCGACGGCAGACACATGCATAAACACAATAGATCAATCTGATTAGTACATAAATAAATTGATCTAGTAAAAACGCTTATCCAGATCAGTGGAAGGAGCAAACTCGTGCTGATAACGTGTTGAATAACTAGTGGCCTATTCGCTGATCCGGAGTAGAAGACGACGATCTCATGCACACAATAGATGAATAATGAACACAGATATAGGGAGAGGCATCACAGTTTTATTGCTTTCTCATATATGTGTATG

Coding Potentia
Explanation CPC Score
noncoding -1.49044
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0253500.1 4 10003277 T C
Osa04LNT0253500.1 4 10003663 A C
Osa04LNT0253500.1 4 10003735 A 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
Osa04LNT0253500.1 osa-miR439a Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439b Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439c Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439d Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439e Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439f Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439g Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439h Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR439i Cleavage 4.0 20.356 1 21
Osa04LNT0253500.1 osa-miR1429-5p Cleavage 4.5 14.845 1 21
Osa04LNT0253500.1 osa-miR1847.1 Cleavage 3.5 23.641 1 21
Osa04LNT0253500.1 osa-miR1873 Translation 4.0 23.719 1 24
Osa04LNT0253500.1 osa-miR5515 Cleavage 5.0 16.935 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0253500.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0253500.1 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0253500.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0253500.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253500.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0253500.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0253500.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0253500.1 4 qCER4-1 Morphological trait Shoot/Seedling RG190 RZ69
Osa04LNT0253500.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0253500.1 4 gwt4a Morphological trait Seed RG788 RG190
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