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

>Osa07LNT0393400.2

GGGAACTAACCGCACGAGACAGCGGGAGGTTTCATATTCATATAGCAGGTAAAAAATACAAGAAACAAGGTTGTGATGAGGAAAAAAAAAGACACCCTTCTAACACACCCACGAGGAAAGAGCAAGCACTGAACTGATGACCTTGTGGCACAAAAGGAACCTCTAAGACTGCTCATAGATAGGGATTGATTTGTTCATTACATGGCCAAAGATAAGAACACTACTCCTAAGTCCAAGAGTGAACATGTAATATCAGTCAGCACCGTAGCATTCCCCGATAGCTTCCACTAGATCCTTTGCTTCACCATTCCTTCCAAAGTGATCACGAACAGGCTGCAATATCTCGTTCAATGACTTTTCAAGGGCCAGCTTCACATCAGCAGGATGCAGAGCGCCACTTTCATAATCAGCTGTAAGTTCCTCCATGCTCAGAAAAGTCTTTTTGCCACCATTCCCTTTCTTCTGGACCACCTCAAACATTCCAAACCAAGGCAAGATGATATATTTTATGTACTCCAAACATGGATTGCCTTCTGCTAGTTTTGGAGGGCAGAAAGCTTTTTCCATTTTAAAACATATATCCTCCTTATCATCTTCCATGAAGATAGCCCAAGCTGGATGCCTCCTGTTCTCCATTTGAGGGTATTGTAATAAATTAGGAAGCATATTGTCCAAAACAGCAATTGCCTTATTCTTCTTTTTGAAATGCTTATAATATTGTCTAGCTAATAAGTTGGCATCATGCTGTTCCATTCCCAACAGCCATATGTCTGCCTTCTGAAATAATATGCTAGCACACTGCAAGCAAATGTAAAAAATCTCATCAACATTTAATTTTCCAATCGCATAAGAATTTCTACTCCCACAAAATCTGCTAGGTAAACAGTAATAAGAGGACCTGCATGTACTTTTTATTCTACGCACACTGTTTGTCCTTGCAATATCCATGACAATTGGCCAGTACTCATCACCATGTTGACGTATTTCATCTGACAACCAGACTAGATCTACTTTATCAAGAGCCATGCCAGTTGCTTTCCACATCTCAATATTGTACCTGCCAACAGTCCGCATCTTATTTAGATTGCCACTAATCTCACTGTTCATCTGGGAAAACCAGTCTGCCATTAAGATTTTAACTTTGAAACCAGATTCAACCATTTTATTAATATTGAGTGTCTTCATGATCCCCTGAGAAATGTGCATCCAGGGGCATGGATCACACCAAACATAACAAATGGGGGCATGTTTCTTCTTTAGCAGTAACTTAAGCTCACGATCGTTGACCCGATCCTCCCCAATGCTCTTCAGTGCTGCAAACCTCAGGTCAAAACTCCCCTCAACAGTATCCCTGAATGTAAACAACTAATTTAGCATGCCAACCTTACAAAGCTTAGTTCAATATTGAAGTTCAGAAGCGAGCAAGGTTATCCATTAGAGTCGACAGCAGCAACAGCTGAATTCTCCATGTTGCCATTACTACGGTGCTTAAGTTCTGTTCGGAGATATAGTCCAGCATTGGCGGAGCTCCTCCCGGGAGCTGTTCTTCGGGGAACTTTTGCCGTTGTGACGGCGTGCTGCCGTGGAGATGACAAAGCTGCTGCTGTGGCATCTGGGAGCGGCGGCGCGGCGAGGCGGAAGCCTCGACGGACATAGTCGGCGTTCGCTTCCATGTTTTGCCCACGAGGCCAAACGCCCGCGCTAGCATTGCCCCCACACGGACACGGGAGCTCCAAATCCAGGGGCGACCGGCTAATCCGGTCGCAGCCTCCGCGCCTGACTTCGTCGACGACGATCGGCCGCCGTCGCCAGGGGTTAGGGTTAGCGGCGGCCCAAGTCTTCCCCCTTATATTCTTTTTCTGTTTTTCTAGATAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.9501
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0393400.2 7 28586087 A C
Osa07LNT0393400.2 7 28586199 T C
Osa07LNT0393400.2 7 28587816 T C
Osa07LNT0393400.2 7 28588355 T A
Osa07LNT0393400.2 7 28588505 A G
Osa07LNT0393400.2 7 28588935 T C
Osa07LNT0393400.2 7 28590386 C T
Osa07LNT0393400.2 7 28591517 A C
Osa07LNT0393400.2 7 28591537 C T
Osa07LNT0393400.2 7 28593022 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
Osa07LNT0393400.2 osa-miR5837.2 Cleavage 4.0 15.699 1 21
Osa07LNT0393400.2 osa-miR820a Cleavage 5.0 23.574 1 21
Osa07LNT0393400.2 osa-miR820b Cleavage 5.0 23.574 1 21
Osa07LNT0393400.2 osa-miR820c Cleavage 5.0 23.574 1 21
Osa07LNT0393400.2 osa-miR1852 Cleavage 4.5 16.096 1 21
Osa07LNT0393400.2 osa-miR1873 Translation 4.5 15.062 1 24
Osa07LNT0393400.2 osa-miR2876-3p Cleavage 5.0 13.459 1 21
Osa07LNT0393400.2 osa-miR5487 Cleavage 5.0 17.97 1 21
Osa07LNT0393400.2 osa-miR1425-5p Translation 5.0 13.098 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0393400.2 7 S23(t) Physiological trait Sterility R1789 C213
Osa07LNT0393400.2 7 qPLLN7 Physiological trait Sterility RM234 RM172
Osa07LNT0393400.2 7 nan Morphological trait Seed RM118 RM248
Osa07LNT0393400.2 7 qDTH-7 Physiological trait Flowering S10832 RM1306
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