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

>Osa06LNT0350700.1

AATAAAAAGAAGCAATTCCTGATAAGAAAAGAGTCCATAGAAGGGTAGGGGAGGCAAAAACCGGTGAACACAATGGCATCTGCTGTATCACGGCCACCAGCGGAATACAAGACTTTCACTTCTGTGAATGCAATCAACGATACTAAACTACCAACTTGCTTTCCTCTTGGTTTATTTTGGCACTGTAGATAGATACTACCCTGACACTGTCTATTTGGTGAGGGCCCCATACAGAAATCCACCGTTTTGGTCACGGAGGACAAGATCTCTCCCCCCTTGCGTCGGGAACCAAGGGCATCAACAAAGCAAGGGAGAAACGGGAAGGAGAGGAGCATCGACAAGCAATCATCTCCCAGTAAGCACCAAGCACTGCCATGTTTGCCAACCTTGTAGTCCTACCCCTCAGCCTGCTGCTGCTGCTGCTCCTCCTCCTTGGGAATGTGGAAGCCTTCGATCTTGCGTGCAACCTCATTTACCCCAACTGTTGGTTTGCCATTTGAATTGACCGCCTCATTGTCATCAGCGTTAGGTGGGCTCAGCTGCCAGATCCGGATGGTGCCATCTTCTGATCCTGATGCATAAGATTCACCGCCAGGTGCAAAGCGGACACAGTGGACAGGACCATGATGCCCCTTGTTACAGGTTATTTCTTCACCAGTGAAGAAATCAAATACATGAACCCACATATCTTCTCCCCCAACAATAAATTTGCTCCCAGATTTTGGTTCCAGGGAAGCTGACTCCACAGTGCAAGGCATATCATAGCTTTTAACAAGCCCAAAGTGATTAGCATCCCAAAATTTAACACTCGAGCCATCAGCTGTAGTGATGAACCTGCTGTCTTGACTTACTTCTGCGCTAGTCACAGGCGCCTTGGTTTCAAGAGTTTGGACAATTTTTCCAGTCCTCACATCCCACAATCTTACTCCTCCCATATCAGAGCACGAGCTTAGTATTGTTTGATCACTATGAAGCCAAGCAACAGTTCGCACGTTACCAGGTGCTTTGTCAAGTTCTCTTGGTGCTGCATCTGGACGATTCATATCATAGACACGCAAAATCTTTTCTACGCCTCCAGTGAGCAACAGGTGGGTATCCTCAGAAAACGCGCATGCACGGACAATGTGCTTGTGTTCAAATGAATGTAGCTCATCACCTGTTAGTGCATCCCAAACTTTGGCTGAAAAGTCAGCAGAACCAGATGCAGCACGCAGAGCATTTGTGTCTAGGCAGCAGCTCCAGACAGCCCCTTTATGACCTTGGAAAGTCCCAATCCAATCTCCAGTCTCACCATTACGAAGCATTGGATTCCCATCCTTACTGGCGCTGATGAGGAAGTACCCGTCGGGCGTGACGGGGCTGTAGAACAGGTCGACGACCGGGCGCGAGTGGCCGTGGCACACCAGCGGCACCGCCACCTTCTTCTTCTCCATCAATCTCAACCCCCCACCTCTTCCCCCCCCCCGACCGACGAAAACCCTAGCTCCTCGACTCCGGCGGCGGCGGCGGACCGAAATGCGGCGGCGCTCCCCCTAACCCTAGGGTGAAGAGAGAGAGAGAGAGAGAGAGAGAGCCCTCCCCACCGATCGGGAGAAAAAAAAATCCGGCGAAGAAAAAAAAATCGCGATCGACGAGCGGCGGAGAGGGGGTGGGCGAGGCGATCCGGATCCGAGGGGGGGATCGATTCGTGCGGGGAATTTTATTGGGGAGAGGAGCAGAAGAGGTGGGGGGGATGAGGCCGCGGCCTAGGTGGCGGGCGCTAGGCGAGTAGCCTTGGGGGGAGAGGGG

Coding Potentia
Explanation CPC Score
noncoding -1.09851
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0350700.1 6 23613287 C T
Osa06LNT0350700.1 6 23613420 T C
Osa06LNT0350700.1 6 23613568 C A
Osa06LNT0350700.1 6 23613986 C A
Osa06LNT0350700.1 6 23614195 T C
Osa06LNT0350700.1 6 23614438 A T
Osa06LNT0350700.1 6 23614840 A G
Osa06LNT0350700.1 6 23615770 T G
Osa06LNT0350700.1 6 23615774 T C
Osa06LNT0350700.1 6 23615998 C A
Osa06LNT0350700.1 6 23616304 C T
Osa06LNT0350700.1 6 23617362 G A
Osa06LNT0350700.1 6 23617751 C T
Osa06LNT0350700.1 6 23617768 T C
Osa06LNT0350700.1 6 23618490 A T
Osa06LNT0350700.1 6 23618691 T G
Osa06LNT0350700.1 6 23619263 C T
Osa06LNT0350700.1 6 23619278 T C
Osa06LNT0350700.1 6 23620807 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
Osa06LNT0350700.1 osa-miR5837.2 Cleavage 4.5 19.896 1 21
Osa06LNT0350700.1 osa-miR156b-3p Cleavage 4.5 20.599 1 21
Osa06LNT0350700.1 osa-miR156b-3p Cleavage 4.5 20.464 1 21
Osa06LNT0350700.1 osa-miR1870-5p Cleavage 4.5 15.413 1 24
Osa06LNT0350700.1 osa-miR3979-5p Translation 5.0 19.43 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0350700.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0350700.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0350700.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
Osa06LNT0350700.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0350700.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0350700.1 6 nan Morphological trait Root RM4447 RM5509
Osa06LNT0350700.1 6 RPLD4 Physiological trait Eating quality RG424 RG172
Osa06LNT0350700.1 6 gw6 Morphological trait Panicle/flower RG424 R2549
Osa06LNT0350700.1 6 nan Physiological trait Eating quality RM253 RM162
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