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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa01LNT0005200.1

TGAACATATAACCATGTACTATTTCTTGCTTGTTCTTCTCTTCTTCTACATCTTGCATTGTATCCGTGTGGATCATGCATGCATTGTCTGGCCCATCTGGTTTGTTAACTTGTTGAGAGCATGCTTGCTTGCACAACAGTACAAAGCCAGATGTGTCCTACAAAGTTGCAGACTTGTAGCTGCACTAGCTTACACATCCATGGCCTATTCCACTGTAGGAATATAAATATACATACACACACACATCTATACAAATACATGTCTAGCTATACTAGCTAGTGGTTCTCATCACTTGCATATATACATACATGCCAGTACAGGATCAGGTTCAATTGCTTAAATTGTACAAGTTCCTATCATTGACCAGCCTGGCTATAGCTTAGCTCGAGCCAAAATGCCAAACAGATTAGTTTAATCAATTAGATGCATAACTAACTAATAATCAGTAACGACAAGCTTGCAGCAACAAAACAAAGCACTTAATCAGCAGCCAGGGTACAACTAGAAGAGACAACACAGCATGTCCTTTTCGTTTTCTTTTCCTTCTTCTTCGATCCTCTTCTCTCTTGCTTGAAGATCTTGATTCTTTTTCTACATCTAGATAAAATTAAGCCTAACCAATAATTAATTAACCACACTTTTTTTTTCAGTTCTGAAATCAGAATAATAATCTTAATTATTGCATGCTTAATTAGATTAATTAATTAATTAATTATCTCCATCTAGCTGTCTGCTTCTCTGCTCTTGTAATTCTTGCAGCTGCAGATGCTAGCTTTGCATGCATGCATGCAAACCATTTTGCATGGAGGAAACCTTAAACACAAGTACCACCATTTTCTCTTCTTTTTTTTTTTGCTCTATTAATTGTTTCTTTTTTTTTTTGCGTGAGATCGAGGTAGCTAGTAGCTATAGCTTATGCGTGGACGTCGGCGGCGGCGGCGACGTCGTCGTGTTCGTCGGCGGCGGCGGCGGCGTCGGTGGAGACCATCTTGAGGGCGGAGCCGCCGGTGGCGAAGGCCTTCTTGCGGACGGCCATGTACTCCGGCCACGTGACAGCGCGGTAGGCGGGGCTCCGGCCGGCCGGCACGGCCTCCGGCAGCGGCGCCACCTCGGCGTCCGGCGGCGGGCCGAGGAAGTAGCCGAGCGAGACCCGGTCGCGGTCGCGGTTCACGACGGCGCGGTGGTAGACGCTGTGGAAGCGGCCGTTGGTGAGGATGTGGAAGAGGTCGCCGACGTTGACGACGAAGGCCCCCGCCACCGCCGGCACCGCCACCCACCGGTCGGGCCCTCGACGGAACAGCTGCAGCCCCGGGACGAGGCTCTGGAGCACGAAGGTGAAGAAGCCCGAGTCCGTGTGCGCGATGAGCCCCAGCGCTCGCCGCGGCTCCGGGCACCTCGGGTACCAGTTGAGGTGCACCGTCGCCGTCATCCTCTCGCCGATCCTCCTCTCCGCCTCGACTCCGGCGACCTCCTCGCCGGTGAGCCCCAGCGCCCTCAAGAACAACCTCAGCAACTCGTCGGCTAGCCGCCGCATCTCCTTGTGAAACTCCTCCATCACGTCACAGAAGAGGAGGTAGTCGTCGCCGGACTTGGGCCAGAGGCGGCGGAGCTCGGAGCGGAGGGAGGAAGGGGAGAAGGTGTAGCCCTCGGACCACATGAGCTTGGAGAAGAAGGAGGAGATGGGCGGCGAGCCGTAGCCGCAGGGCTCGCCGGGGCCGCGGACGGCGCGCATCTTCTCCGACGCCGGCAGGGAGAACACGCGGGCGACGCGCTCCTCGACGCGCGACAGCAGCGCCGCCGGCACGCCGTGCCCGACCAGAAGGAACGCGCCCCACTGCTCCGCCGCCCGCGCCACCCGCGCCGCCGCGTCGCCCGCCCCGACGTCCACCACCGGCACCGCGTCCTCGCCGCCGCCGCCGCCGCCGTCCACCACCGGGTGGTCGTCCAGCCCCGGCCACGCGTGCGTCTCCGGCACCCGCCTCGCCGCCCGGAAGTCGAAGCAGAGCGGGTTCTTCAAGTGCGACGGCGTCGGCATCGCGACGACGACGACGATGACCAGAGAGCAACACACTCGCGCGCTCGCTCGTCTCGTCTGGCAGAAAGCCAGTAACAATAACAACACTAATTTTTTCTCTCTATATAAATTTTTTCTATGACTTTACAATAGTGGAATGAGTAGTAAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.470698
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0005200.1 1 4003431 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
Osa01LNT0005200.1 osa-miR5531 Cleavage 5.0 15.552 1 22
Osa01LNT0005200.1 osa-miR5789 Translation 5.0 24.288 1 21
Osa01LNT0005200.1 osa-miR6256 Translation 4.0 7.254 1 22
Osa01LNT0005200.1 osa-miR426 Cleavage 5.0 10.364 1 21
Osa01LNT0005200.1 osa-miR2926 Cleavage 5.0 23.229 1 20
Osa01LNT0005200.1 osa-miR2926 Cleavage 5.0 24.733 1 20
Osa01LNT0005200.1 osa-miR2926 Translation 4.5 21.082 1 20
Osa01LNT0005200.1 osa-miR812n-5p Translation 4.5 21.733 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0005200.1 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0005200.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0005200.1 1 nan Physiological trait Source activity RG532 RG472
Osa01LNT0005200.1 1 gp1a Morphological trait Panicle/flower RM1 R753
Osa01LNT0005200.1 1 qFLL-1 Morphological trait Culm/leaf RZ543 RG532
Osa01LNT0005200.1 1 qFLP-1 Morphological trait Culm/leaf RZ543 RG532
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