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

>Osa01LNT0004000.2

GAGATAGAATGCATATGTAAATGGGTGACTTGTATAAAAGGAAAGTCACAATTTTCAGCAATAAATGAAAGAGAGGTGTATTCGTAGCGACTCAATTCTGCAGGGAATTCGGCTGTACATGAGTATTTTGATTGAGTTGTATTCCCTCCAGTAGAAACTTACAAATGTACATCCTTAGAGAAAAGATAAGGAGGAAGACATAAAATAGAAAATGGCGGCGCACGAAGAACGTCGCTTTGAAGAATCAGTAGTTACATTGTGATTGCGGTATCATTGATTTTACTGTTTATGTGGTAATTGAGTCTTCCTTCTGTTCAGAGGATGCAACGGCAACAGCACTGCCTTGCTCATCCCCTTGACCCTTTTCTTCATCAACACCCTCATCATCTGGGATCATCACTGCCTTCACCTGTGCAACAATAACCGTAATGTCATCCATCTTACCACCTATTAGTTTCCCTCCAATGAACTTTTTCCACGAGGGGACATCAAAACCCCGACTCCGAGCCTCCATTGAGTAGGGTGAATCAAAGGTGACATCCACTGAATGCTTCCTTGCAAGCTCTGCTAGTGCTTTTGCAGCTTCATCTACCCCTGGAGACTCGGAAATGACAGAAACGATCTCTTGATCGAATATATTGTCAAAAAATCCATCTGAGCCACTGACAATCATATCACCCTCCATAAGATTTACTGTGCAAACCAGTGCATCCAGATACGTTTGACCAATTGCTTCAGAGCTTAACTGGTATGGGCAGTCAAAGTAATGTTCTTGAGGACATGTAGAGAACATTACTTGGCCTTTTCTAATTACTTTCAAACCACAATCTCCCACACTTGCAATTTTTAGAATCCCTGTCTTCTCAAGCATTGCAATGATTACAGTTGCAGATCCAACAGAAGTTGTTGCAGCATGAGCCTTCATTAGAAGAAGCTGAGGATCATGATTGACCTCCTCATCCTTGAGAAAAGTAGAAGTGTGTGCCATGAGCTCTCGAGAAAACAGAGCCGGATTGACATCCTTTTCTGCCCATCTGTCAGTAGACAAGAGAATGACCTGAAACTCCATCTGCGACGGCAAACACTCCACCATCATCGCCGTTCACAAAGAAAGCATCTTCTCCGCCAGTCTCAGCCTTTCTTGGGTGTGGTATTAGATGAGTTCCAATAGTTAACACAGCTTCCAACTTGGCGGCGCGAAGAGGGGAGAAGCGCGAGCGGCGAAGCGGGAGATGGGGAGAAGGGGTAGTGGGTGCGTGGAGGCGAGGCGGCGAGAGGCGGGTAGCAGTGGAGGAGGCCGCCATGGCTGGCTTGCTGCTGCTCTATCTCCTCCTCGCCTCGCCTCCGTCGCCCGCGGCCACCGTGAATCGCTCGCTCGCTC

Coding Potentia
Explanation CPC Score
noncoding -1.25166
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0004000.2 1 3334260 C T
Osa01LNT0004000.2 1 3334443 A G
Osa01LNT0004000.2 1 3334542 C T
Osa01LNT0004000.2 1 3334728 T C
Osa01LNT0004000.2 1 3334987 G A
Osa01LNT0004000.2 1 3335107 T C
Osa01LNT0004000.2 1 3333734 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
Osa01LNT0004000.2 osa-miR5541 Cleavage 3.5 16.759 1 21
Osa01LNT0004000.2 osa-miR5828 Translation 4.0 20.047 1 21
Osa01LNT0004000.2 osa-miR5832 Translation 4.0 14.359 1 21
Osa01LNT0004000.2 osa-miR5832 Translation 5.0 11.308 1 21
Osa01LNT0004000.2 osa-miR167c-3p Cleavage 4.0 18.271 1 23
Osa01LNT0004000.2 osa-miR2097-3p Cleavage 3.5 23.081 1 22
Osa01LNT0004000.2 osa-miR2877 Cleavage 5.0 22.867 1 24
Osa01LNT0004000.2 osa-miR2927 Translation 4.0 18.581 1 23
Osa01LNT0004000.2 osa-miR5488 Translation 4.0 9.117 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0004000.2 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004000.2 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004000.2 1 nan Physiological trait Source activity RG532 RG472
Osa01LNT0004000.2 1 gp1a Morphological trait Panicle/flower RM1 R753
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