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

>Osa01LNT0004600.1

CCACAATGCCAGAGATCTGGGCCTGTCTATATATTTTTATTTTTCAGAATATTCTGCAAGATAACATCAATGGTACTCAATGGACGTACAAAGAATTGCCAGAGCAGCTGCTATGTTGTTAACAAGTTATCTATGGTACATGTTCGGTAGGACGAAATGATCATCCAGGAAACTAGAGCCTACTGACAGCAAGAGCATTGACATATCAAAAATACAGTGTGTTGAATTACAACTTCAGATTTCCATACCCCTTCTTGATCTTGCCTGTATAACAAGGGAAGAAACAACTAAAGCCTATCTCAAAGTTAAAACTGTATGATATTGCCGTGCCGTGCTTGTCGATACTGTTTTTTCATTTCTTTCCATTGGCATAGGGGTACTCTGCAGGTGAGCTCCATAAGCCAAACAAGATGGAGATGTGAATGAATAGCAACAGCAGTGACGAATAGGCAGTGGAAGGATAGATATTCCAGCAGAGCTCCACAGCAAGAAATAAAATGACCCTCACAAATGTTGGAAAACGAGTTTTCCACAAAAGGAAAGGCAGTGAATAGAAGTACCAGGAATAAAATTGGTAGTGTAATGATCGTGCGCACACGATGCCAATGAAATTTCCAACAAACATGACCGTTACAATATGTTCTTTGTTAAGAGTTGACAGTTTGGGCTTGGCAAAAATTAACTGTCCAATTGATGTGGCATCTTTGAATCTGGAATGCAAGAAATGGAACAAGCCACCCTCATGCTTAAGCCACTTGTAGTGTGCAAAGACCAAAAGAGTAGTGAGGTGAAGAACCAACAATGCAACAGCTAGCTCTTTTGATACAAAGAACTTCTCAGGGACAAATTTAAAATTTACAGACCAGAAATGGATGAAGACACGCCCAAGATTGAATGCTCGTGAGATGTACTCAACTGGATGTGATAACAAGAATGGCATACCCAACAAAACCTGTAGTGCTGCAGCCCCTAATAAAGCAAAGAAGACTCCTTTGATGCTCATGGCCTTCAGCATCAGTAGTAATAACGATGGAGCAAAAAGAAGCACATTCATCTTAATGGAGACAGCTGCACTGAAAATTACTAGACCAAGGTACCACTTGTGATACATAATCAAAACCATGGCAGCATGGAGAAACGTCATAGCGAAACAATCGTTGAAAAGGCGGAGCACAAAGATGGAGTGAACCCTCTTTGACAAGCAAAGCAAACCTAAAGCCCACCTTGGAAGCACTTCAGTCTTGACGTACATCAGCAGAACAAGGCTAAGGTTCACAATGTACAGGACACCAAACAAAATCTGCGCGGGGAAGACTTGGCCGGCGGTGAGAAGCTTGATGGCGGAGTAAACGTAGAGGAAGCCGGCCGGGTAGACGAGCGGCCCCGTGTCGCCCTCGATCTTGGTGTAATCCCTCTCCCCTTCCACAAACGCGTCCACCTGAGCCATGTACGCGTCCCAGTCGATCTTGGTATACGGGACGAAGACGACGATGAGGGCGACGAGCGCCGCGTCGGCGAGCAGCAGGAACGCCGCGAAGTGGAGCGGCCTACGGTCGGACGGCGGCGACGACTCGCCGTGCTTGCCCACCCGCGCCATGGCCGCCTCCACAGCCAAGCTCCGGGCAGCTCGAGGT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.904562
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0004600.1 1 3705435 A G
Osa01LNT0004600.1 1 3705520 C T
Osa01LNT0004600.1 1 3706018 G A
Osa01LNT0004600.1 1 3707112 C T
Osa01LNT0004600.1 1 3707662 G A
Osa01LNT0004600.1 1 3708840 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0004600.1 osa-miR6252 Cleavage 3.5 14.254 1 23
Osa01LNT0004600.1 osa-miR156f-3p Cleavage 4.0 18.199 1 22
Osa01LNT0004600.1 osa-miR156h-3p Cleavage 4.0 18.199 1 22
Osa01LNT0004600.1 osa-miR156l-3p Cleavage 4.0 18.199 1 22
Osa01LNT0004600.1 osa-miR1875 Translation 4.0 23.02 1 24
Osa01LNT0004600.1 osa-miR1863b.2 Cleavage 4.0 15.91 1 23
Osa01LNT0004600.1 osa-miR5500 Translation 4.0 14.577 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0004600.1 1 nan Physiological trait Source activity RG532 RG472
Osa01LNT0004600.1 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004600.1 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0004600.1 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0004600.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0004600.1 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