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

>Osa12LNT0138400.2

GATGAAAAATCACCATCTTATTACTCACTTTTATGCAAAGACCAAACCAGACAATGAGTTCAATTGCCTCGTCCAAGTACAGCGAGTTCAGTACATTTTCTGTTCCCAAAAAAAAAATGATGCCTGAAGTAGCTTGTGCTTCTCATAGTTTTCTTTCTGCAATGTACTACATAGAGGCCTCATTTTGGTTGTAACATATACCCAATCCATGGGTTACATACAAATTCAAACTAGTAGCAGGCAACTCCAATGTAGTGCCGAGTTGTCAAGACCACTTCTTGCTCAATAGTTTCGATATGGTCAAGTCAGTACCACCAAATCCATCCATGACGGCCTTCGCAGAGTGAAACTCAGCTCTGGCGGTTAGGCTGCTTCTAACAACTATGCATGGCATACCAATGCGCTCAGCTGCAAGAACGCCAGATTGGCTACCTGCGACAAGAACACAGTTTTGCACGTCCCGTCCAACATACTCGGATCCAGCGCGTAGAGTGACAATAATCTTCTCGGAGCTTTTAGACGCTGCATTGATATCAACACTAAGTTTCAGAATGGACGCAACTTCTTCTGCTATCCTCTGCTTTTCTGCAGAAGCAGCCTTTTGTGCTTCCTTAACTAGCTGTTCATCCAAACTGGAGGCTACTCCTTCACCAAGAACAAGTTGTCCATATAAGCTTCTTTCAACCTCTTCTTTCCCAACAATATGTATTTTTGATGTTCTCTCTTGGCCTAATTTTTCAATGATATATCTTGAAGTTTTCTCTCCATTTCTCCCGTATGTTGTCAATATGGCGACAGGCACACCCTCATTAAGCGCATCATCAATGAACTGTTCAACTCCAGGCCGCAGTGGTAAGCTATCAGAAGCTGAGAACACTTCCAAAGCTTTCAGCTTTTCACGAAGAACACTTTTCATAAATGATTCTTTCTCGTTAGTTGGCAAAGAAGTAGGCCACCCAATTCTGTTGAAGAATAATAACAACATCCTTTCCTCGTCGCCACTAGCTTTCCTCACTAAATCAGCATATATTGGCTCTGTCCAATTTGCACAATCCAGCCCAAGATTTTGAAATGCTACATTGAAAGCTTGGCGATTGCCGAAGCGATACACATCTGCAAGAACTCCTTCCACTTCGAGGAGCACGGCGATATCCGGCGACGCGGAGCCCTGCGACGACGAGGAGGAGGAGGCGCACCGGAGCGGCGGGATACGGCGGCCGGAGCTCGGGGGAACGGCGGCGCGGAGAGGGAGAGAGGCGGCCGCGGTGGTGGTGGAGGAAGAGGAGGAGGAGGAGGAGGAGGAGGCAGGGATGGAGGAGGAGAAGGCCTTGGCGACCTCCGGCGGCGAGGCCCGGAGCGGGAGGCAGCGAGCGGCGGCCATGGCGGAGAGGAGAAGGTGCGCGTGAGCTTTTGTTACAGTAATAACGTTTTCAAAGAGTACCACACCAAGGAAATTATTTAACTTGTTGACGTAGTGCCTGTCTTGCAAGACACGGATTGTTCCTGTCAAAGGAAATAAAAAACATTCTCGAGCCAATCCACCAATTATATTCATCATCTCGAAAAACATAAATATCACAATCATTTACAAGAGAGAATTTTTTTGAAAACAGCTTTTGGTGAGCTTCCATGCATTTTACAAGAAGGTGGTTGAGAGCATATGCATTACACGGTGTGAATTATTATCATTTAGGCCCCGTTTGATTTAGATTATTAAGCTAATTATTATTATGGATTATCTACTATAAATTAAATATTTTGAGAATAAACTTAAAAAATAGCTTAAAATAAATGGACTAAACAAAAATCAATTTCTAGAGCTATCCATATTCCACAGTATGAACTAAATTCTAGATCACTCAATTCAATCAGAAGATACAGTGACAAGGTAATGACGTAATGTTCCAAAATAGAACTCATATGCCATTTGCAAACATCTCGACCTTCTACATACAAATCTAAAGATCCACTTGTACTAATTCAAGTTCATTTATCAAGCATATTAAACGGATAGCAAACGCCAAGCTGCAGTATGAAAATAGCCCGAATTTTAAATGATTTCATAAGTAATTACCAGGGGCCACTCAAAGTCTAGTTCGTCACCTTGCAATATTTTACCAACCAAAAAGCAAATTTCAGGAAATATTTCACTTGATGTAGATTATGGTAAGTAGGAGCAAGAAAAACTCAAACCGTGTAATAGGATCATGCCCAGCAAATCCATCTTCACTGTTTATAGAGCCAGTACACGCGGATTAAAAATTAAAGTTCAACAAAGTTCAATGGATTTACTCTAGGTCTCTAGCAAACCCCTCTTGATCATAGCCATGTGCTGGTGAGGTGCTTGTATGATGTTCTTGATGTCCCACATGGCCATCCAGTTGGTGTTTATCATTTCTAGCACAAACTTGATGTCCTCTATTGAAACAAAGTCTAAGTTGATAAAACAAAGGACATAAATCTGTGGATTTCTGATGGGTATTAAGTTGGTACCCTACTTATAGCTTTCAGCTCTCATAAGAGTGTGAAGGTGAAGAAATCAAAATAGCTACATAGAACGGACTGAAATCACTGTATTTTACATGGGTGTAAAGTTGGTACCCTTTTGTTGCTTTCAGATCTCATAAGCTGATGTTTTACTTGACCTGGACAGCATGTGCCTCACTCGCACGCATCAATGAAACCAGATGAGACAAGTCTTCAGCAACTGGGTTGGAGGGGACTGCTACCTCATGCGTGACCTGGTTGTATCATTGACGACCAGCTAAGAGACGGGACATCCAATGGAGATCACTGTTGCTGGTGTTGCTGGTGTCCTTATTTGCTAGCATGAATGATGTCCAACGGCCCTAGTCCTGTGCCCTCGTTCCAGCGCATCCCTCCAGTCGGCACCCTCTCCTACGACCGCGCCGGCGGCCTGCTCCTCCCCGGCACCTCTGTTGGCGCTCGCCTCTTGCCCAGCCAACCTCGCCGATGCTGACGGGCCATGCGCAGCGACCTCCAGCCCTCCTCCAATGGCCCCCTCTCCTCCTAGCAAGACTCTCCGCCACCTCATATCCCCTTTCCGGCGGGCGGCACCCGGATGTCCGGCCCGCGCGCCGGCGCGCGCGAGGAGTCAGCGGGGTAGGGGGAGCAGAAGTGCAGAACCCGCCTCTCTTTCCTCTCCATCGCGGCGCGGCGCGGCGCGAGCAGGGAAGCAGGCAGCGGCGGGTAGGGTGAGGCGGCTCCGGCGGGTGCGCGCGAGGAGGAGGCGAGCAGCTCCGGCGGGAGGCGGCGGCAGCGGGCTGGCGCGCTCTAGGAGGAGTCGAGCGGCTCCGGCGGGAGAAGGCGGCGGCGCGCTGGAGCACAAAAGGGAGCGTTCCCTTTCTTTTTTCTTTGACC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.448223
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0138400.2 12 26998229 T C
Osa12LNT0138400.2 12 26998242 G T
Osa12LNT0138400.2 12 26999238 G A
Osa12LNT0138400.2 12 26998086 T C
Osa12LNT0138400.2 12 26999686 C T
Osa12LNT0138400.2 12 26999868 A G
Osa12LNT0138400.2 12 26999906 T G
Osa12LNT0138400.2 12 27001274 G T
Osa12LNT0138400.2 12 27001826 T 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
Osa12LNT0138400.2 osa-miR2873c Translation 4.5 8.936 1 21
Osa12LNT0138400.2 osa-miR160f-3p Translation 4.5 20.007 1 21
Osa12LNT0138400.2 osa-miR417 Cleavage 4.0 15.774 1 21
Osa12LNT0138400.2 osa-miR417 Cleavage 4.5 9.435 1 21
Osa12LNT0138400.2 osa-miR1850.1 Cleavage 4.0 15.582 1 21
Osa12LNT0138400.2 osa-miR2103 Cleavage 3.0 24.806 1 22
Osa12LNT0138400.2 osa-miR2931 Cleavage 4.5 16.114 1 20
Osa12LNT0138400.2 osa-miR5490 Translation 4.0 9.259 1 21
Osa12LNT0138400.2 osa-miR5508 Cleavage 4.0 17.261 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0138400.2 12 qDRS12-1 Resistance or Tolerance Drought tolerance RG181 RG958
Osa12LNT0138400.2 12 qLEI 4 Resistance or Tolerance Submergency tolerance RM5479 C901
Osa12LNT0138400.2 12 nan Physiological trait Eating quality RM235 RM17
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