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

>Osa09LNT0427700.1

AAAGTTCTTCCCAAGCTGCTTCAACAGTTGACGTATACCTGCGGCTAATGTATCATCCTGTATGCAATGCTTCAAGTCCTTTCTCAAGTCGGATTTTTTCCTCTCGAACTCTTCTGTGAACTTCTGAAGTCTTCTGTTCACAAGCTCTCCCAAGGACCTTGAAGCAACAGATGGAGATATCCTAGCAGGATTTCCAACTCGTACTGTGTCCAGTCCAGTATCTGACAACTTCTCCACCATGTTATCAACTGCTGCATTGCTTGGAGCAGTTACGAGAACGCGTTCACCCTTTCGGACAGCACATGCAATGAGATAACTAAGCAAACCAGTCTTGCCCGTGCCAGGAGGTCCTTGGATTATTAGGACAGGCCTTTTGTTGTTCAAGCCTAGTGTGATAGCTTTTAACTGGGAGGCATCAAAGTCATATTTGTTCTTTTTCAATAGCTCATCATCATGTATTGTTGATTCTCCCCAATCAGCCAGATTATTCTGCTCCATCATCATCATGTCTTCCTTGTCCCCAAACAGAGTGGCTACTACTCCAATGGAAGAATTCTTTTTCTGTAAACCTTTCCTTTGAAGAAGCATCAGTGCTTCACAATTTCGCTCATATGTAAGTGCGTCAGCCAATGCCTGAATCCTGTCAATCCGCACATTTTTCCCAAAAAGCTTGGAGAACGTAGGATCACCACGGCGGGATTTCAGTGTCACGGTAATGCTGCAACCATCCTCACCAAGATTATATATAAAGCCTTGCATGCAAGATGTGGTAATTTCCCCCCGGTTATCACATGTCCTGATACAAACCATATCCCCAGGAGAGAGTGTGGTTGGAGGCAATCTATGGTTATCTTTCACTCTAAATAGGACCAGATGCTGGCCATCCAACCCAGTTGAACTGCTGATAACATTCAAATTGCAAATGGTATCGCACTGCTCTTGCTGTGACTGCCCATGAGTGACTAAGTACTCTACTGGTTTGAGTGGCTTCTTTGAGTTCCCATCCATCACAGGGGTGGCATTCAGTTCTTCTTGTGTAAACTCCAGCTCCGCATCTCGTTCTATATGTAGAAGGTCTGACATTTTCTTGACAAAGTCTTCAATTTTGGTCTGCATCAACCTTGTCTTATCAAGACTTATGCCAAGAGTACTGTGCGTAGTAGGAGCTTTAGGTTTGCGGGCAGCTGCTCGATGCTGAGCTGAGTTAGCCAATTCTTTCAGAAGCATCCAAGATTGAGTGGTGCGCCAATCAGAAATAAGACCCTGGTTCTGTTGTTTCAACAGAACATCACGGAGTTCCCTTTGAAAGTGGTCAAAGAGGGTAGGATAGTGAGTAGAGGCCTTGAGGCAGAGCGCCTCCTGTCCCTTGGGCATGGGAATTGCTGATAGATAAGGCTGTGCAAGCATCACAAATCCGAGGTTGTCTTCAGATGATCCACCATCCAGTAAGAATGTTGCTCCATCGTTCTGCATTTCTGTGGAAGCATATTTTATAGCCATTGAGTGCATACCCTGCTTTAGCCATTGTACCACGCACCGGCCCAACTCCTTCTTCCCAATGGGGTCGCCACTCTCATAAAGAGTATTTACCCTAATGGACACTTCCTCCGCAGATGGAACACACTCCCCTTCATCTTTTGCTGTCTCCTTCCTCTTTCTCCCCCTCCTCCTCCTCCTTCCTTCCTTTCTTGTACCGTTATCAGTGATGCCATGAGGGAGAGAAGAACGGGAATCAGCCGGAAGTAATGTTTGTTCTCTAGGTCCTGCAGATGAAACTAACAGGAGATGACTTTGCTGTGAACAAGTGTTAGGAGCTGAACTAGAGCTGCAGGGAAAAGATGGGAATGGAAGCAACTTCAGCTCTCTCCTCCTTAGGTGCAGTGCAGTGGCACGAGAAGAAAAGAACCTGAAAGACAGAACATGAGAAGACATGCTCAGCCCAGGAAAGCTAGATATGGAGGCGAGAGGAAGACGAGAAGAAATCACTACCAGTAAGTGAACTTAAAAGGAAAATATTGACAGATACAGCTACATGGGCATATGAGCTTAGGACTCAGGATTTCTCACTGATATTTTGTAAGCTTGATAGCCATGCTGGTGACTTGCAGAGTTGTGGTGAAGGCAAATGCTACGTTACCTTCAATCCATACATATACTAGCACTGGTGTTTACCACTTCCGTAGCTGTGCAGTCTCTCTGTGTTGTACACGTTTTCTCCAGCTACACCTTGCTCCATAGTCTCTGAAGCTCCTCACAGTTCAGTTCTAACCCACCAATTGCCATGCCCTTTTTGATTTTTCACTTATCCCCATCCATTCCATTCCAATGGAAACACCACCACCACATGTTAGCAGGCGACACACATCCTTTCTATATGTGTTGCGTTAAGAATCACATAAAATTCCAGGGTTAATTGGATCCATGCTACTGCAATTTTGCCAAATTAAAAAAATATCACTGCTATTCATCATATCGGCTACGTGCCACTGGAAATTTCTAAAATTGGAACCATGCTACTCCAGTCACTTTTTTCATCTCATCTCTCACGCCGTCTCCGTTCACATCCTTATCCCCCTCCTCTCCACGGCCACGGGTGGC

Coding Potentia
Explanation CPC Score
noncoding -1.05093
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0427700.1 9 2357646 A T
Osa09LNT0427700.1 9 2358161 A G
Osa09LNT0427700.1 9 2358187 G A
Osa09LNT0427700.1 9 2359083 G A
Osa09LNT0427700.1 9 2359937 G A
Osa09LNT0427700.1 9 2360445 A G
Osa09LNT0427700.1 9 2361220 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0427700.1 DTM_#DNAt_MULE_japo_Os0284 Chr9 - 2361122 2362257 191
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0427700.1 osa-miR159c Translation 5.0 7.833 1 21
Osa09LNT0427700.1 osa-miR159d Translation 5.0 7.833 1 21
Osa09LNT0427700.1 osa-miR1425-3p Cleavage 4.5 18.285 1 21
Osa09LNT0427700.1 osa-miR2871a-3p Cleavage 5.0 19.456 1 21
Osa09LNT0427700.1 osa-miR2871b Cleavage 5.0 19.456 1 21
Osa09LNT0427700.1 osa-miR2919 Cleavage 3.0 16.141 1 19
Osa09LNT0427700.1 osa-miR2919 Cleavage 4.5 12.716 1 19
Osa09LNT0427700.1 osa-miR395x Translation 4.5 7.854 1 21
Osa09LNT0427700.1 osa-miR5492 Cleavage 3.5 12.832 1 21
Osa09LNT0427700.1 osa-miR5518 Translation 5.0 7.078 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0427700.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0427700.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0427700.1 9 nan Morphological trait Root C711 G103
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