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

>Osa12LNT0113800.1

GAATAAAAAATTAAGTAAACAAATAAACTTGAATATGACAAATATTTGCAGTTCACAACTTCAAGTAAGGATCTATGGATATATGGCTTCTCTAGCAAACTAACAGAGCCACAGGTAAGTTCTACCATTGAGGAGCCCAAAAAAGTTCTTTCACTTGGGCACCTCTTTAAGTAACAAATGTAATGCCGACATTTGTTTGCCTCAGGACTAACAATAAGATCTGGCTATGCAAACAAAAGTAAAGTCTAACTAACTTCACATAATCAAGAAGAGTTGAACAAACTCCTCAGACCAAAAGGAACAGTTGTACATCACATAAGCCGCAAGCCTATCCTACAAATCCTCCCAATTCATAAGCATTAATCCTGCTTCACGATGCAGGACTCGCCAACTATCAGATCAATCCTCAGGGATTATTGTTTAATATACAAAGTTAGCACAAGGTGCTTCCTTTATAGCCCAACAATTGTTGTAGAATCATCATTGCCGTTGGGCAGATGGAGATTGCTGAACCTGCACTGGTGGGAAGAACCCAGCACCTGGTGGTTGAAAAAATCCAGTCGAGGTCGGCGATTGCTGTGGTGCCTGTGGAGACTGCTGCTGCTGGGGCTGGCTCTGGTTCTGAGATTGTGTAGGCAGAGGCAGAGGTGGAGGCACACTTAGTCTTGGAAAACCTGCTGACATAATGTTGGGCAATGGGGGTGGAGGTGGCGCAGAGCCACTCACCATCCCAAAAGGTCCCATTCCAAACATTCCTCCAGTATTTTGAACAAATTGTGGCATAAGTGGTAATGGAGGTGGAGGTGGTGGAAATGAACCAGCTGCTTGGTTTGCTTGGGTTGGTGGCTGTGTGCCTCCAAGAGCAGCTGTTGCTCCAATCTGTGGTTGCACCTGCGGCAGTTGCCCAAAGAATGGGGGAGCACTCATGTCACTAGCATGAATGGGGTTGTCAAGCCTAGGCTTCTTATTGCTCTCAAAGCCTGGAGGTCCTGCAGAAAGATCTCCAGAAGTCGAACCACTATTCCTTGCTTGTTCAGCAGCAAGGGAAGAGAAAATGGAGGAGAGCACCTTCTCAGGAGCTGACAAAGATGCAAGCTTATCTGCCATAGCTGCTGCAGTTTTTTTGGGCTCATCACCAACAGCACTGGATGTGGCAGGAAGTGAGGTTGCTGGATGCAGTGGTTGAAACTGGGGAAATATCGGCATTGCTGCTGAATTCTGCATCATGGCAGCTGTTTGTCCTGGTGGAAGTGTAACCATCAGTGGACTAGAACTAGATCCTGCACCATTGTTCAAGGCACTACCAAGTCGTTGTTTTAGTTGCATGGCATGTTCAGCCTTTGCTCGAGCCACCTGTTAATTAAATCAGGGTTAGCCAAAAATCAATCTAAATAATTTCTTGAGTAGCTGCTAAACCACCCCTTCAGTGGCAGGAAAGATGCTGTGGTTTTAACTGAGATGGTAGATAGCAATGTTAACAAAAGCCAGCGGAGATGGATACTACATAGGGAACAGAAATATGTGATTGGAAATTTCTAACTTAAGATGCAATGACACATGTTTGCACCATGGAGTTAGCAGGTTAGCTACATAGAACCTAGGTTACAATTAATAACAATGCATGCGCATGGGTATATCACTGCAGGCATATCTTTATATTAGCTCGTGCAAGGGCCACCTTAACCGTATAGCTTATGCTGTAGAGATAGTCAGACCTCCCAATGTGCTGGACCTAATTCTCTTGAAACAGATAAAGAGAGAAATGTCATATATAAGCAAACATAAGTTGGAATTGAGAAGCAGTCTAACAAGTAGGAAATGACATGTTGCCTTGTTATCCAGAGTAGGCCTCAGGGTTGCCATGGTAACTTTTAAGAGGCAGGTTTGTGCTTGAAGCAGGATACTAGATGAGCCAGACATCATCTGTGCTGCCCAAGCTGACCATGGTTAGTCTACTACTTCCATCATAGAGCTGAATTGTACAGCAGATTCAGCAACTATCCAGTTTAGAGGCTTCTCTTCGTGTCAGAGCATACAATGTGCATCTTATGTGTTCTCATTTTTGCTTTTGTATTTCCTAGCTCTACTCATCCTGAACATGTGTGATATAAATTCATGAATGAATGTCGTTGACAAAGCAAAACTCTGGTTGTGCTCACATGCCATGGACTCATGGGGTCTTAGGCTAGGCATCAAGAATAGAGTCTAGCTCAAAGCAAATACAAAAGCATATGGATCCATGAAAATGCTCAGCATAATTTTGACCCTAACTTTCCATTATAATTGAGTAATAACAGACATGGCATAAGAAATAGAATGATCTAACATGTGATTCTGCAGTGAAAGATGAAGTAATATGCATAAAAAAATAATCCTTACAAGCAACTGATTGCGAAGAAGCTCTGACTTTGCTTCCTGTTATAAAGAAAGAAAAAACATAAAGCTTTATGACTGTAATAGTATGCCGTCAAGGTAGAACATTTGGAAGAAAATATAAAAGGTGCTCAAGACCTGTTCGCCGAGGGCTTTTCTTAGTTTATTGATTAGGGTTATTCTAGCCATGTTGACACTTTCAAGTTGCTCAATGCACTGCTTAAGGACTGTTTCCTGCCCTTGAAGGTCAGAAATCAACGATGATCCTTGCTGAATACCTTGAGTACAAGCATCATCTACATCTTTATCCATCCTATCCAAAACACTAACAGCATTATTGCATTTGTTTAAAGCTGTGTCTTCATCAAAATGTTGATCAAGCACTGACTGATATGCTGTTACAATCTTTTCTGGCATCCCGCCAACAGTAAGTTTTCTTGTTACTGTACCAGAATCTTTCCGCGCAGCTTTGGAAACTGAAGAGGGGTTAGGGCTTGGATTTGAGCTATTGACATTGTTACCCATTGTATGAGTGCTACCACCAAGAATGTCATTTTTCAGACTTTCAATACGGGTTCCAAAGACCTTCCGCTCATCCCAAATATCTATTAATCTTCCAACTACTTTCTTTCCATCTTCTCCCCCATTGACATAAAAGTCTTTCAATAATCCAGGAAGAACCCTCCAAAATTCATTCACAAACTCCCCTCCCTTGCGTTTACTATTTTGCAGGATATCATTTGACAGGTACAGGAATGATACTTTCTTATCCTTATTTGCACTGTTATACTGCTTCTCCCATGTATCAACAACCTTTCTGGCTCTCTTTCGGTGAAAAATGCACCAATTTGAAAGTGCTGCTTAAGAATTAAGGAATAAAAAAGGCATGCTATTGTAATCTAGATGCTATTGTTAAAAATATGCTGTGGGAATTTGGTATCATGACTGTGTAAATGATTTTTACGGCATTGACATCAAACACAGGAAAGCAAGTGGTAAGACTCGTTCAGAAGATATTACATAGGGATTCGAGTTGCTAATATGTAAGCAAACGGACATGACACAACCATCACATAATCCCCCACCCCCTTTGTAGCGTGAATTTATGGATGCAAATGGATAAATGCTATATATATCCTTCTTCAAATGCCAAAAATTTGCAATTTGCGACTTGTTTTTTTTACAACCATAGGGAATCTGTTATTTGTTTAATTGATGACAGTATATGATAAGCCCTGACCTAACTGCTTAACTGATTTAGAAATGAAGATAAATGGTCATAAAAGAATCGAAAAGGTTGTTTATTCATTTGCCAGTACTACCTCCGTTCAAGAATATAAGAAATTTTAGGGTTGGACACGGTTATTAAGAAAGTAGGTAGAATTAAATGGAGGAAGATTGTGATTGGATGAGAAGTGGAACTAGGTGGGAAAATTGAATGGATGATTGTGATTGGTTGGAAAGAGAATGTTAGTGAAGAAGTTGTTATATTTAATCATTCCTTTGTAATTTTGTATTTTCTCCCTCTCTTCCTTTTGTAAATCTTTTCTTATTAATTATTTAATATAGCGCAGTAGGAGCCCCTCCTGCTGTTCCACGTCAAAAAAAAAAAAGAAGTTGTTGTATTTTGGGACAAATTCTGAAGGCTAGAAATTGTTATATTTTGGGACGGATGGAGTACAACATTAGTGCAACCAAATATTACCACATTGTATTTCGAACATAGATTAATGGATACCATCGTAAAAAGCAGTTCCACAAAGATTGTACAAGAAGCCATCAAGAGACCAAAAAAAGTAGAACTAGCATATCAGTACCCTGATAGCAGCAACCAAAAGGAAACAAAGTATGTGATATATGATTGATTCTACCCATTAGTTTGTAAATTGAACAGGAAAACAGCTATATTCAAATCCACAAGAGAACACTACTACAATGTGATACAAACCTAACGCTCCTTATCATTACTCCCTCTGTTTCATATTATAAGTCGTTT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.972268
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0113800.1 12 1292986 A C
Osa12LNT0113800.1 12 1294493 T C
Osa12LNT0113800.1 12 1294594 C G
Osa12LNT0113800.1 12 1297650 A C
Osa12LNT0113800.1 12 1298107 T C
Osa12LNT0113800.1 12 1298505 T C
Osa12LNT0113800.1 12 1295941 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa12LNT0113800.1 DTM_#DNAt_MULE_japo_Os0115 Chr12 - 1295484 1295984 500
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0113800.1 osa-miR5534b Translation 4.5 16.119 1 21
Osa12LNT0113800.1 osa-miR5541 Cleavage 4.0 15.604 1 21
Osa12LNT0113800.1 osa-miR5837.2 Cleavage 3.5 9.041 1 21
Osa12LNT0113800.1 osa-miR6248 Cleavage 4.5 19.684 1 21
Osa12LNT0113800.1 osa-miR6248 Translation 4.5 14.371 1 21
Osa12LNT0113800.1 osa-miR818f Cleavage 4.5 17.002 1 21
Osa12LNT0113800.1 osa-miR1437b-5p Cleavage 4.0 19.869 1 21
Osa12LNT0113800.1 osa-miR396a-3p Cleavage 5.0 21.581 1 20
Osa12LNT0113800.1 osa-miR396b-3p Cleavage 5.0 21.581 1 20
Osa12LNT0113800.1 osa-miR167d-3p Translation 4.0 14.146 1 22
Osa12LNT0113800.1 osa-miR413 Cleavage 4.0 12.329 1 21
Osa12LNT0113800.1 osa-miR413 Cleavage 4.5 13.24 1 21
Osa12LNT0113800.1 osa-miR1435 Translation 4.0 11.83 1 20
Osa12LNT0113800.1 osa-miR1435 Translation 5.0 14.708 1 20
Osa12LNT0113800.1 osa-miR1436 Cleavage 4.5 7.467 1 21
Osa12LNT0113800.1 osa-miR1441 Cleavage 4.0 14.197 1 21
Osa12LNT0113800.1 osa-miR1439 Cleavage 4.0 17.319 1 21
Osa12LNT0113800.1 osa-miR1439 Cleavage 4.5 7.467 1 21
Osa12LNT0113800.1 osa-miR1864 Translation 5.0 14.856 1 24
Osa12LNT0113800.1 osa-miR1866-3p Cleavage 4.0 16.773 1 22
Osa12LNT0113800.1 osa-miR2863a Cleavage 5.0 8.44 1 21
Osa12LNT0113800.1 osa-miR2871a-3p Cleavage 4.5 12.253 1 21
Osa12LNT0113800.1 osa-miR2871b Cleavage 4.5 12.253 1 21
Osa12LNT0113800.1 osa-miR5144-5p Cleavage 4.0 21.974 1 21
Osa12LNT0113800.1 osa-miR5161 Cleavage 4.5 7.467 1 20
Osa12LNT0113800.1 osa-miR5487 Translation 4.0 18.421 1 21
Osa12LNT0113800.1 osa-miR5487 Translation 5.0 10.69 1 21
Osa12LNT0113800.1 osa-miR5492 Translation 4.0 13.37 1 21
Osa12LNT0113800.1 osa-miR5492 Cleavage 5.0 15.992 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0113800.1 12 nan Physiological trait Eating quality RM20 RM101
Osa12LNT0113800.1 12 gy12 Morphological trait Seed RG869 RG98
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