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

>Osa01LNT0002500.1

GTTCTGCAGTTGGAGGATTTTTGTTTTCTTTCAATATTTCTGTACTGCCTACATTGTGGAATTTGTGGTCACTGATTGTGAATCTAATATCTGATACTGAGCTTTATCTGAAGAGACACTTAAGATTGAAATCTTGTACATTAGTTTCTGGTACACAGCCACAGAAACCTCCTTTTGGTTTCACATGCAGCCATTGTAAGGTATGATGTAATTCTATGAACAAAGTATACTTGGGCCGAACACTCTGTCTTCGCCTCCGGTCTTCGGACATTGTAAGGTAAACATCTCTCTACTTATCTTGTTTCATAGAGTCTTGATCTCATGCTTCAAGCCGTAGTCAATTCTCTAATGAGTAAAATTCTTCTGCATCTTCATACACACAAGGATGGGTGGACAGTGGAACAGGAGGTAACTCTTCTCTCCTTTCTGGCAGAAACCAAGAATACACTTCCTTTGCCCTCTGTACCAAAGGCCTCTCAACATTCTCACACCAGGCGTCAAACATATCGAGGACAGCCTCAGTAATGACTTCTGAGAGTACTTTATCACCTTCTCCAGGTGCCAGCTTCAGCATCATGTATCTCTTGAACGATACGATCTTCTCTAACATTTGCCTTCTGTCAATATTATATGATGACATCGCGCCTTGGATTATAGAGACCATCCTGAGGACTGCCTCACAGACTATAGCATATGCATGACTGAATATCTCGGTTGCTGTTTCTGACAGTTCTTTGCTGTGCCAATCATTTTTTACAGGTTCTGGCCCCTGTTCTAAGATTGGCGCAAATGTTACAGTCTTCGGTTTGGTTGTGTTGACACGGAGCTGCTTTGATTCCCTCAGCATTTCATTGGCTTCCTTCATTTCTGACTCAAACCTGCTGCTGACCTTGAAGTATGGTTGCTCCTTGTGTGCAGTTGGGCTCGGGAGTGGGGAATTCTGCCTTGATGATGCTTCCAAGAAAACCTCAGGTGCACATGCTGATTCACACGAGGAATGGGGATGTCGAGCTGTGCTTGGGGATCCGTAGTCTGCATCGTTGTGCTCCTTGCTGTCGTCTGCACTGGGTCCTGCTCGGGGGGTCCACATCATGTCTTCTTGCGGCTTCTTCTTGTGATGCAGCAGGTGCATCCATTTCTTAGCCTTGCTCTTCACCTTGCCGAGAACTGGCTTCTTCTGGCTCCCATTTGGGGTCCGCGGCGATCCCATCGGACTCACCGGCGGTGCCCGTGGCGAAGGCCAGTATCGTTGTTGCTCCTCCCATTCATCGACTGGATTTTGGCCTGCAATATTCAGAGACGCATTTTGGACGGGGTGATCACCTCGTTTGGTGCTGATCCCGCGCTTCAATTTTCTGATTTCATTCATGATTTGTGCAAGAATGGAACCAAATCCTAGAGCTTTGGGAGGAGCTGATCAGGCAAGAAATGGACTCTATCCTAAAGTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.798547
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0002500.1 1 2388632 G C
Osa01LNT0002500.1 1 2388760 G C
Osa01LNT0002500.1 1 2389069 T A
Osa01LNT0002500.1 1 2389149 T C
Osa01LNT0002500.1 1 2389404 A G
Osa01LNT0002500.1 1 2389524 C T
Osa01LNT0002500.1 1 2389632 T C
Osa01LNT0002500.1 1 2389724 G A
Osa01LNT0002500.1 1 2389989 C T
Osa01LNT0002500.1 1 2390130 G A
Osa01LNT0002500.1 1 2390201 C T
Osa01LNT0002500.1 1 2390292 G A
Osa01LNT0002500.1 1 2390303 A 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
Osa01LNT0002500.1 osa-miR5795 Translation 4.5 19.826 1 22
Osa01LNT0002500.1 osa-miR812v Translation 5.0 17.884 1 24
Osa01LNT0002500.1 osa-miR166a-5p Translation 5.0 12.329 1 21
Osa01LNT0002500.1 osa-miR166e-5p Translation 5.0 12.329 1 21
Osa01LNT0002500.1 osa-miR3979-3p Cleavage 4.5 19.659 1 20
Osa01LNT0002500.1 osa-miR2275c Cleavage 3.0 14.691 1 23
Osa01LNT0002500.1 osa-miR2275c Cleavage 5.0 12.81 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0002500.1 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0002500.1 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0002500.1 1 gp1a Morphological trait Panicle/flower RM1 R753
Osa01LNT0002500.1 1 nan Physiological trait Source activity RG532 RG472
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