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

>Osa04LNT0252200.1

TCCACCCTCCGCGCCCACGATCCCTTCTCTCTCTCTTGATCGAAAAGCGATGGCGGCGGTTCCGGCGCCCGCCCTCCTCCCTACCACGAGCGGCTGCGGCGGTGCCCTTCCCCCTCTCCCCGCGAGCGGCGGCGGCGGCTCCCTCCGACCTGTCTCGCTTTCCTCGCCGGCGGCCGCTCCCTTTGTCCTGTCTCGCCTCCTCGCTCCCTCCTCCTCTCCTCCTCGCCTCCCTCCCGCGGTGGCGCGGGTTGACGGCGGTCGCGGGCGAATCCGAGGGTGGTGGCGGCGGCTCCCTCCATCCCCTCTAGCCTTCCTCCTGTGGCAGATCCGCCGGCGGCGGCGGCCTCCGCAGGCGGATCAAGCGGCGGTGGCTCCCTCCGCCCCCTCTCGCCAAGTCCCGCGGTCGATCCGACGGTGGTGGCGGCGTTGGCGGCGTCCGCGGGTGGATCCATTAACAGTGGCGGTGGGCAGATCCGGTAGCGGCGGCTCCCTCCGCCGCCTCTCTTCTCCCTCCGGCGGCGGTGGTGGTGTCGGCGGCGGCCGCGGATGGACCCAGTGGCGGTAGCAACGGCCGAGGGCAGCGGTGGCAACGGCCGAGGGCCACGGTGGCGATGGCCGAGGGCGGATCCGGTGGCAGCAAATTTGGAAACTTCCTCCACGCAAAGCCGTAGCGAAATTCTCACCTCAAGATGGCCCTCACCGTCGGCCACCTCCAGCCGCCACTCGCCGGAGCCGGAGCCAAAAGCGTCGCCATTCCCGGCCCACTCATCCCACGCCGCCACATCCTCCTTGCCGACGCCGACGTACTCCATCCCCGCCACCCGGTGGCCGAACCTGACGCAGTCGAGCACCCCGAAGCGGCGCGCGTAGGCGCCGAGGTAGTCCATCACCTGGCGGTGGTCCGGGAACACCTCCGTCACCGTCTCCGGCCACGGGAAGTCGGAGTACTGGTACATGGGCCGCGGAGTCTGCAGCGCGGTGCCCTCCAGCGTCCACGCCCACACGCCACCCACGCCGGTGTCCGCCTCGAACACCACCGGCCGGCAGCCGCGCTCCAGCAGTTGCTTGCACGCGGCCAGGCCGCTCACGCCGGCGCCGACGATGACCACCCGCTTCTTCTCCATGATGGCTAGTGGGCTAGGAAAGTGCGAGCTGTGTGAGTTGTTTGGAGTCTGATGAGCGAGGTGGTATTTATAGTTGGTCAGTGCTATACTTCCTCGAAATATATCTTTTGACCATGTCATCTAATCATAATATATATAATGGATAAAAATATTTTTACTGTTTTTTAAAAGTTATATATATGTAGTGTTAATACCTTTAAACTATATTTTAAAAGTTATCGATGATCAAAGTTACAAAAGTTTGATCTCAACTTTATCTAAAC

Coding Potentia
Explanation CPC Score
noncoding -1.11305
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252200.1 4 8267597 A G
Osa04LNT0252200.1 4 8267759 G A
Osa04LNT0252200.1 4 8267855 T C
Osa04LNT0252200.1 4 8267890 A G
Osa04LNT0252200.1 4 8268148 T C
Osa04LNT0252200.1 4 8268222 G T
Osa04LNT0252200.1 4 8268290 T C
Osa04LNT0252200.1 4 8268373 A G
Osa04LNT0252200.1 4 8268705 A T
Osa04LNT0252200.1 4 8268775 T C
Osa04LNT0252200.1 4 8268449 T G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0252200.1 osa-miR5793 Translation 5.0 15.74 1 21
Osa04LNT0252200.1 osa-miR5819 Cleavage 3.0 23.597 1 21
Osa04LNT0252200.1 osa-miR1858a Translation 2.0 9.325 1 21
Osa04LNT0252200.1 osa-miR1858b Translation 2.0 9.325 1 21
Osa04LNT0252200.1 osa-miR2102-5p Cleavage 4.5 21.162 1 20
Osa04LNT0252200.1 osa-miR2878-5p Translation 4.0 10.762 1 24
Osa04LNT0252200.1 osa-miR5074 Cleavage 5.0 19.46 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252200.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252200.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252200.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252200.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252200.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252200.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
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