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

>Osa07LNT0393200.2

TATAGGAACAAAAGTATACATCATTCAGTTAAGTGTTCAGTCATCCATGAGACTACAGAGGGGAGCAGCAAACTTCTTTAGCAGCAACAGCACATATCATTCTCATTTGGGTATGTTGGCCCCTGAATATTCAGTAATTAAAACCCAAATGAAAATCTAAAAGTTGGCAACATTTATACCCACTTATCTAGGCAGCAGGCTGATCTGACTAGATTGGAAATGAAGCTCCTAAAGCCTGCAGCCATCTAAAATAAGAACTTCATTATTTAAGCTAGTAGTACATTATTATTATTATTATTTCCACTATATCTCAGACTATTAATTTCGGTTAATTGTAGTAAGATTGCATATCAAGCAAGCACAGAAGCATACTTGCTTATTTACCAAAGTTTTACATGCCGCATTCAGGATCCTGTGGACTGAAAAAGCAGGCAATGACCTTGGAGTTCAGCAGCTTCAGTGCAAGGCTAGATTCGATGCATCTGGGTGTCTTGTACTGGTTAATGGAGCTGCCATGGCTAACCAATAGATCCATCAGAGCATCAAATGCACCAGCTTCAACAAGCCGTATCTCCAGAGGCCCTATGGACCTGTCATGGGCTCTGCAACGACGGTAGACGTAGTCCAGTGACTCCTCGACAGCAGCACAGCAGCTCTCGAGGAGCTGAGCGTCAAGAGGGGCCGGCCTTTCATCGTGGGTGGACTTGATCTCCCAGAACAGCACGTAGTGGCCAGGGACAGTGGAAATATCAGTGTAGCTAGTGTACTCCAGGAGGAGGTAATTTTGGTTCTCCAGGATTTTCTTAGCAGTGGTGACACTGTTGTGGAGATCCTCCTCGTTGGTCTTGTCAGAATCGATGCTGAGGATAACATTTCTCCGGCAAATGAATTTGAACTGCGGAGCTCGGTTGTAGAAGCCTGTCACTTGAAGCACATCACCAACCCTGTACCTGTAAAGACCTGAAAATGTGGTAACTACAAGCTCATAGTAACATCCAACCTTGACATCTACCAGGCTGACAAGCTTGTCATTCTCTATCACCTCCTCGTGATCAGTCAACCTGAGGCCGTCCTCTAATGGTATGAACTCAAAGTAAGCCATGTTTGGGAGGATGGTGTAAGACACATCAGCTGGGCTACATAGTGGACTCAGATTGACACCGAAATAGCTTTCTGAGGAAGCATACATCGTGCAGACGAAAGGAATCGCACCACCACCATAGAATTCCAGCATGGGGATATATTGTGCCATTGTGCCCGTAAGAACAGCTTCGATATATTTAACATTAGGCCATAGCCTTCCCAGAATCCCCTTCCATGAACCGCAGCTGCATATTGCCTCAACCTGATCAGCTAGCTCTGGGTTGGGCAATGCAAGGAAGTTCAGCATGGCCAAACGGCATGCTGGACTGGTGATACTGGAGTTGAGCTGACCAATTCGTATGTCATTGACAAGGTCACGCCAATGCTGCTCAAGGAAGCTGATAGATCGAAGGAATGCTGAGGCAAAGACTGCCCCGATACGAAGAACATGCTGGCGTTCTACCAGGCCACAGAGCAGCTGGCAGTACATGCTCTGCTGGCTATCAGGGCAAAGAATGACCTCATCAGGACTGGTATAGTTGTTGTATAAATCGTGTTTGCGGTGAAGGAAATGAGGGCTCTTATAGTAGCTAGTGAGGACTGATCGAACTGGAATTCCAGAATCTGTCAGTGTTTCAGCTTTCACAAAGAGAAGGTACATAGCTTTCCCCTCACCAAGGCCTGATATATACCTTTGGAAGCATTAATAGTGTGGATTTTAGAAACACCAAAACAGCTGTGTATAACAGTTGGTTTCTTGATGTGGTATGAGGTAGCAAATGTATATCTGGCATTGCCTGATACTTTGCTAAAGCAGCAACCAATATATGAACTTATTTTTAAGTTTTTGAGCTGCAAGCAGTGGCATATGCGGTAACTATTGTCCAATACTTTGCGTCTTGCAACTGGAGTACTGGACCCAGGTTGTGTTACTAATGTGAATAATCCAAAAAAAAATGTCAAACAGGAAGCATGCAAAACAACGCCTCTCAGGATCTGTCAATTTTAGGGTCAGTGTCAACAGAGCTTCACAAATGATATCATTTGTTCATGATAGGCATGATCAGACTATAGAGGTAGGTTCGACGGTCAAGATCCTTTAAGATGGACGGCATCAATCTTGGCTCACCTCGAGAAGTCCCCGAGCTTCTAAGCAGCTCCAAGATATATTCTCCACATAAAATTGAAGATTCCTCACCAGTTGCAATCCTGAGAATGTATGGATGTACCTTATCATATGTTACTACAGGAACATGTCTCTTGAAGGCAGAAATATTTGTTGACCCATTCATGAATTTGCTCAGGTACTCGGTAGCCTGATTCCTCTCAAGGATTTTCGTCAATATGAGCTCTTGGGCTTCTTTGGCATTCACTGTTAACATCTCAAGCTCTTCAAGAGCACCACTTCCCTTGTAGTCTAAGTTATGATCATCCATATTACGAACAAAAGCAGAATTACAGTCAACCTTATTTCAAAAGGGGAGGCGGGGGCTCAAAGTAACGATACTGGGAGCTTGTTTGCCCCTTATATAGTGTGGTGATGCATGGTCTGAGAAGCATATCTTCTTAATATTTCGACTTTATTTGAAAGATTCTGAACCAATACGACGGTGCAGCCTGTGCAAGATGATCCACTTGCTATCTTTCTGGACACGACAGTGTCTCAATTTATGGAACTCCCTCTAGTAGTGTTCTATTGAAAAGTGTAATGTGATGTGATAATATGTTGAAAACTTAAAAATTATATCAAGACGCTGTCCTCCATTATCCATTGCCTTGCTTTGCTGTGTGACGCAGAACTCCACCTGTTTCTCACGATGTACCTTTAAGAAGGTCCCCTTTGTCATGAAGAAAAAATATGAAATATTTGCACTAGTCTTGAAATATCACTACAAACTCCTAGCCATGAAGAAAACATGAGGCATGTAGGGATAGGCAAAAGACACTATACTTGGGTAACCAGTAAGTAAAGGGCAATCTTTTTGTGGTAATGATAGAAAAAATAGGTTGGAAAAGCTAGAACTGAGTTGAAGATCCTAGGAGAGGTGAGTGACAAAAGTGTAAACCTGATCCACTTCCATTTTTTGAATGAAATGTTTTATGTATCAAGAAAAGGTGAATAGTACCATGCCATGGATTGTGGTTAACAAATTAATAACAAATGCACCACCTAGATGAAAAGTTGTAACTTTTAAACCAGTTGGATCAAAAGGACATGATTAACCTCAATCAAAGGAGATGGATAATCTAGCGGAGACTAAGTAACAAAGGTAATAAGAATGCAAACAAAGGGTTGTGGCTGACAGTTATTGGTTCTTCATCCCAGGAACTTCTATTATTTGTAGTGGGTCAAGTGACTGATGCTAACCAGAGTCTCCACTCTCCAGAAGCAGAGACCATCTACAATGCTCAAAAATCATAATATTAGTATTGTGGTCAAAAGGAGTAAACAGAAGAAAAAAACATGTTTACATTGCCACACAATCCCATGGACCTAAGCATGAAGCTGCTGGCAAAAACAGAACAAAGTTTAATTCATGCAAAAAAAAATGTGAACTCTTTTGACTGCAATTTCATATGGAACTGGGCATGGAGATGCTGACAATGACAAATCAAAGCACATAGACCACAGGTAAACAATATTCCAGTGGAAAAAAAAAACATCCACCAAGATGATGAGGCAAAAGGTGCACACACAATAATGATATTTGTCAGATCATGATAAAGTTGTCAATAATGCAACTAAGGAATACACTGCCGTGGTACAAGGTCGCACACAATGAAACACATCAGTAAAGTAGATAATACTGGAGACAATAACATATTTTGTACACTAAAAAAGTTATTCCAGGAAAGTTGTAACAGCATCTGAAGGTTTCGTGTAACATAAGGCGTTAGAAGGGAACAATGCTAGCCTTAGTTTGCAAGGTCCCAAGGTCACTGAATCAACAAAACATACGGCTATAAACAAACACCAAATTCCATACTAGGTGCATCCCCAACTTGAAGCATCCAAGGATGATTCAATAGTAAAAAGAACAGGTTACTCAGGAAGGTAAAGAGCCTGCGCATGCATATGCTCAAAATATCAGTACATCAGCTGAGCTCTACTGACTTACACCTGCTACAAAGGTGGCAGCTGCAGATTATTTCACATACCAATTCCTTTCAATTGAATATCACATTATCACAATAGAAAGCGGAATTCTACCGTACCCCTAGCCATTTTCAAAAGGTGATATCGATGGAATAAACGCGTAGGTGACAATCCCAGGCATCATACTTTCTTTATGATATTATCTAGTCATTTCAGGGTAAAGGCATGCATTTACAGTATGCGGATGCTCGCCGCATATGGTGCACTCCCTGTGGTGGTGCCATGCCCCCTGCTCTTCGTCTATTAACTACCTTCACAAAAAAGGGGAAACGGTGCACATATTCTTTGCTAAAGTTGTAAGGATTAATCAGGAAAGATGAGTTATTGGATCCCTTGTAATATCATTATTGTCATATATCCCCAGATTTCTTTCTCCTTGTCCTTGTGAGATCTATCTAACCTTCTCGCTCCACAACAGAAACTAATGAAAAAAAAAACCCCTTCAAAGTGGCCTGCATCCTCCATGATCTGAATAGCCACATGTGCAAGAAATGAAACATTCAGCAGCTATTATACATACATGCTTCTTGAGCTTCGACATTTTACCAAACACTAAAATGCATCCACCATGCTTCTTGAGCTTCTTAGTGGGCACAGCATTAGGCAAGCAGAGCAATCTGCTTCTTTCAAGGTAAAAAGGGCATATCTTTCCACGTTCATGTTCTCTAGTATAGTTCACTCAAGTCAGCATCACCATAAAGCTAGCGATTACGTAATATCTCAAAAAAATTCTCAAGCAAGCATCTCCTGTTTCCATGTCTCCTAAAGTTTTTGGAGAAATACATCAGAGCTAAACCAAAGGTAAAGCAAAAAAAAAAGTCAATAACTTAAACTAAATTGTAGCACAGCATTAAAAAAAGCTGGATATGAAAGGAGGCTATCATATCGATGTTATTAAGAAGGAGGTGAGTCGATTCTCACGCAGGCCAATCGGGTGCGCGAGCGACGGCGGTTCTCATTGTAGCACAGCATAAAGGTGGGAAAAGACCAAAGAAGGGGAGGCTGAGGGAGGAGGGACACTTTCATGATGGAGGTGCAAGCATGCCTGTGAGGGGAATGAACTGTGCTGAGGCAGAAACAAGTCAGAGATTGGTGCCCCTTTCTTCACATCAAGAACAGGGACAGCCAGGAGGGAGGCCAGGCCCCCTCCCTCCATATCTCATCAGTGGTGTTTCCCCTCCCTAATAACCTAGCATAGCTTCTCTTTGGATTAGGATGGTGGGGGACATCAAAGAA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.803875
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0393200.2 7 28395337 A G
Osa07LNT0393200.2 7 28392325 C T
Osa07LNT0393200.2 7 28393221 G A
Osa07LNT0393200.2 7 28393373 C T
Osa07LNT0393200.2 7 28393689 T A
Osa07LNT0393200.2 7 28394048 A C
Osa07LNT0393200.2 7 28395360 A G
Osa07LNT0393200.2 7 28395623 A T
Osa07LNT0393200.2 7 28396058 T C
Osa07LNT0393200.2 7 28397070 C A
Osa07LNT0393200.2 7 28397727 A C
Osa07LNT0393200.2 7 28397935 C A
Osa07LNT0393200.2 7 28398571 T G
Osa07LNT0393200.2 7 28398762 A C
Osa07LNT0393200.2 7 28399292 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
Osa07LNT0393200.2 osa-miR5794 Translation 4.0 17.132 1 21
Osa07LNT0393200.2 osa-miR5796 Cleavage 5.0 17.51 1 21
Osa07LNT0393200.2 osa-miR399a Cleavage 4.5 13.231 1 21
Osa07LNT0393200.2 osa-miR399b Cleavage 4.5 13.231 1 21
Osa07LNT0393200.2 osa-miR399c Cleavage 4.5 13.231 1 21
Osa07LNT0393200.2 osa-miR399d Cleavage 5.0 13.231 1 21
Osa07LNT0393200.2 osa-miR399j Cleavage 5.0 13.231 1 21
Osa07LNT0393200.2 osa-miR399k Cleavage 5.0 13.231 1 21
Osa07LNT0393200.2 osa-miR418 Translation 3.5 11.654 1 21
Osa07LNT0393200.2 osa-miR1850.2 Cleavage 4.5 14.054 1 21
Osa07LNT0393200.2 osa-miR1864 Translation 4.5 12.344 1 24
Osa07LNT0393200.2 osa-miR1882e-3p Translation 5.0 16.865 1 24
Osa07LNT0393200.2 osa-miR2090 Cleavage 5.0 16.899 1 22
Osa07LNT0393200.2 osa-miR2095-5p Cleavage 5.0 14.841 1 22
Osa07LNT0393200.2 osa-miR2275a Cleavage 4.0 18.258 1 22
Osa07LNT0393200.2 osa-miR2275b Cleavage 4.0 18.258 1 22
Osa07LNT0393200.2 osa-miR5073 Cleavage 5.0 17.178 1 23
Osa07LNT0393200.2 osa-miR5490 Cleavage 4.0 14.066 1 21
Osa07LNT0393200.2 osa-miR2927 Translation 5.0 23.911 1 23
Osa07LNT0393200.2 osa-miR5498 Cleavage 5.0 22.307 1 21
Osa07LNT0393200.2 osa-miR5076 Translation 4.0 14.064 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0393200.2 7 nan Morphological trait Seed RM118 RM248
Osa07LNT0393200.2 7 qDTH-7 Physiological trait Flowering S10832 RM1306
Osa07LNT0393200.2 7 S23(t) Physiological trait Sterility R1789 C213
Osa07LNT0393200.2 7 qPLLN7 Physiological trait Sterility RM234 RM172
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
Osa07LNT0393200.2 7 28392325 Grain-length(mm) 11.15179539 -
Osa07LNT0393200.2 7 28397070 Grain-length(mm) 11.44851112 -