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

>Osa10LNT0073500.3

TCCAGTCATCCAGACATATCAATACCAATGAGTAGCAACTCACAAAAATATACAAGGTTCTGAATTCTGATGCATCTTTGATTCTTTACAGAGTAGACGAGCAAAACTTTAATCCGAGACAGGCATATATATGAAGTATACTGCTACTTCTGGGCCTCTGCCTGTTCAAAGTTTACCTCTGAAGTAGCTAAAAGCTCTACGGGGAAAAAAAATCTCAACTGCTCTGTGCACACTACACTACTACAGTCAAGATGTACAACTATATATTTACAAGGAAAACATACAAAACTTTCCACATCAAGCCGTCAACCGTGTGCGATGTGAGCCTTTGTGTGCTAGCCAAATCCGAACTGTGCGGTCATCACTTGCCGAAGCCAGCATATGTGGCTTAGCAGGATTCCAGCTCACACAATTTACAGTAAGTGAATGACCGTATAAGACCTTTATTGGCGTCTCCAGGTGCCTTTTCCAAATGTAGACCTGGGAATCCTCACTGCCACTAGCTATGAACAGAGAGTTTGATCCACCAAAGCAAGATCTAATCACAAACTTTCCTTGCTTGTGTCCCTTGAATTTATTATCCGCCGCAGTAGAACTTTCACTGATTCTCCACAAATGAATTTCCTGGCTGTTGAGGTTGACAATCAGTGATTGTCCATCACCAGAGAGAGATAGCGACGAAATCGTCTGCTGCTCACGTATTCTCCATTCCCGCCCCTTTGGAAGTTCTCGAATCCAAATTTCATTGGAACATACACAGATAAGATGTTTGCTATCAGGAGTCACAGCTATATCACTGACTTTAGGTATTCTATCTCCAACCCATGATTCCAGTTCTTGACCTTCTAGGTCACAAGTGAAGATCCTCTTTGGAGAACTTTCAGGCTCACAGCTGGCACATACTATTTTCTCCGAATTAGGGAACCATGCACATGAATTGATAATATGGCCAACTGAGCTGCTAAATTTAAGACTGCATTCACCAGTAGCAACGTTCCACAGTTTTACTGATTCTCCATTACCACAAGTGAGCAGCATTCTGTCATTTGGGCTCCAGGCAACAAAAGAAATTGGATTTTTGTGACCCACGAGGCAGTGCTTCTTGGTTAATGTATCATCCTCTTCCACCTAAAATCATCTTTGGGGGTTAGGCATGACAAGAATTTGGAGTTGTAAAGCAAGGAAACAAATGATTATGAACCATCAAACCTGGGTTGCCACTTGCCAGTAAGAAACAGCAAGGAAGAGAAGGAAAAAAAATGATTTTAGCCAAACGATAGTTAAAGAATGCATATTATCTGTCATCCTTTGTAACTTTAGAACAGCTGTAATACCCCACCTCAGAGGTGCCTTCACCTACTAACGAATGGATTTTCCCATTCACATACTTAAAAAACATCTCCCATCTAGCTTAGAATATGTGGCCTCTGTGATTACTAGAACATGGAAAATTAACAACACTTTTAGGCATGTACCACATCTTCAAATGTGTACACAAGGACTGTACAATGTCATCAATTTGTGGACTAAGATGTAAAAACAAATTCTGCCCGAGCTCGACTTGTACAAATAAAGTCCAATTACAAATGAAGACAGGTATATATATATATGACCTTTCACGAGCATCATTGATAAACTTTTCCGTGGACATAAGTTGTATGTGGTGACTGGCAGGAAATGCACTTTAAGCTTACCCCTATTTGGCATTTCAGACATTTACCATAGTATCCAATACTTAAAAATTCATATCAAATTTTTCTGGTAACATTTTTAATAAATAAAGATTTACATTATGAAGGGATTTCTCATAAAGTATATGTGTCAGTTTCACAGGGGAAAAATAGCTCCGCTCATCAGTGGACAAAGTTTAAAATGTATGATTGCACGTATCGTATAAAAGGCATATACTTTCTATAAAATATCTTATAGCACTAGAAATTTATGTTTTCTTCCATACCACTAAGTTTCAACATTTATCCTTTTTGCACCACTCCCATTAAACCTGTTAGTTTCAGCTGCCGTTAAGTCATTGGAAGCTGTCAGATGTTTTTTTCCCGAAAAGACAGTCATACCTCAGTCAATAGTTGCTGGCCCACATTATTGGAAACTTCAAGCTTCTTCTCCTTTCCTCCATTCCTCTTCCTATGGTGGAGAGGGAAAAGAGCTTTGATGGAGGTACAAGAGAAGATTAGCAGCAACAGGAATTGGGGAGTCTATATCACACTTTGGCACAAGGCTAGATTGAGGGATGTTGCATTCTCTAATCAATCAGGCTTGTTCTGTTCTCCAATAGCTTTCTCTATGTGAGTTAAACCATTACCAAGTATGGATTATGGAAGATGGGTTAAGTGGAATGCATGGCTTGTTCTGTTCTCCAATAGCTTTCTCTATGTGAGTTAAACCATTACCAAGTATGGATTATGGAGGATGGGTCATGTGGAATGCATGCTATGTTTTGCATGGAGTTAGTCTGAATGTTGTGGTCCAGAAGTGGTTAAAGTTATAAGATATTTTATATATTAAAAACGAGTTGACTTATAACCATTAGAGTTAAGAAGACCAAGTTGTAAGTCGTATTCTGAAACAACAATAGTGAAAAGCATTGTTAACAGCTGCTTTGGTGAAAGGCATACCTTCCATATGATGGCCGTGCAATCACTTGAAGATGATGCCAGATAGTTTCCATCATTTGAGAACCTTACAAACCAAACTTCATTGTTATGACCACATAATATCTGAATAGTAATCCCCTCTTGGCTAAAAAAGAATCTAATAACATTATTATCATTGGTTTTGAAGTATCTCAAGTTATGATCATTTCTTTTAGAATATAACAGAATTTGAAAAATCAGAACTCCACAGAAGACCTCTACACAAGCAGATAAAACATAGTTTGAAAGCAGAGTAGAAAAGAAAGGTTTGAAGTGGTGCTGTTTACAGTGTTTCTATCTTTCAAAACAAAACCGAGATTTCAAGTGCAAAGACTCTTAAATAATGCAAATCCCTGCCTCACTGGGGCTAGAGAATATGCAGTACTTTTGAAGAGTAGTGTCTCCCGGTAGCATGATAATTTTATGCTTCCAAACATTGGCACGGAAAGGATAAAAGCTGCATATATATTGAAAAAATTACAGTGAATATTCGAGTTACTGAGTTAGATAACCATACAGAAGTACGTTCTGAAAACTAGTCAGAACAATTGCCAGCATAAAAATTGTACATTGTCGGCTCTAGTTTTTGAAATTGATCTGATTTCACATACTTATAAACCTTATAACTGGGGTGTTTGTGCAAAACTGGTAATACAAATCAACAATTTAAACTCGCACCTGCGAACACTTGGAAGGAATCTGCTCTTCAGGGCACTTATGATCCTCAAACAAAGTGACCTCGTCCGGTAAATTGTGATATACACAAGACGAAACCTGCTTAACAACTGCATTCTCCACCAGAAGCTCTAGCCGACCGCTTGGCACATGGAACCATGGCGGGAAAGCATCAACCAGATCCAAGAAAAGCCCAATCCTCCACCCGACCACGGCATCCGGCGCGACCGCCCCCTCGCACGAGACCATTGCGCGTGCCAGCCAGTGCACACACTCCCTGTCAACGCCGAGGGGCGCAATCCGGCGCCAGAGCACCTCCCTGGCGCGCGGCAGCCCAGCGTCGCCGATCCCCAGAAGCTCCAGGAAGTGCCCCCTCCACACCAAGA

Coding Potentia
Explanation CPC Score
noncoding -1.24659
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa10LNT0073500.3 10 17159281 G C
Osa10LNT0073500.3 10 17159409 T C
Osa10LNT0073500.3 10 17160074 T C
Osa10LNT0073500.3 10 17161061 T G
Osa10LNT0073500.3 10 17161485 A C
Osa10LNT0073500.3 10 17161550 C A
Osa10LNT0073500.3 10 17161854 T G
Osa10LNT0073500.3 10 17161938 C A
Osa10LNT0073500.3 10 17162482 A G
Osa10LNT0073500.3 10 17158986 A T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa10LNT0073500.3 osa-miR5542 Cleavage 5.0 16.931 1 21
Osa10LNT0073500.3 osa-miR5798 Cleavage 4.0 19.182 1 21
Osa10LNT0073500.3 osa-miR5825 Cleavage 4.5 16.47 1 24
Osa10LNT0073500.3 osa-miR5825 Translation 4.5 14.236 1 24
Osa10LNT0073500.3 osa-miR396a-3p Cleavage 5.0 12.722 1 20
Osa10LNT0073500.3 osa-miR396b-3p Cleavage 5.0 12.722 1 20
Osa10LNT0073500.3 osa-miR396c-3p Cleavage 5.0 12.722 1 21
Osa10LNT0073500.3 osa-miR169q Translation 5.0 20.544 1 21
Osa10LNT0073500.3 osa-miR440 Cleavage 5.0 15.026 1 24
Osa10LNT0073500.3 osa-miR1862a Translation 4.5 20.424 1 24
Osa10LNT0073500.3 osa-miR1862b Translation 4.5 20.424 1 24
Osa10LNT0073500.3 osa-miR1862c Translation 4.5 20.424 1 24
Osa10LNT0073500.3 osa-miR1320-3p Cleavage 5.0 17.614 1 21
Osa10LNT0073500.3 osa-miR2929 Cleavage 4.0 17.03 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa10LNT0073500.3 10 qLSVB10-1 Morphological trait Panicle/flower RM258 C677
Osa10LNT0073500.3 10 qLVB10-1 Morphological trait Panicle/flower C677 RM258
Osa10LNT0073500.3 10 nan Resistance or Tolerance Drought tolerance RM596 RM271
Osa10LNT0073500.3 10 ssd10 Morphological trait Panicle/flower RG257 RZ583
Osa10LNT0073500.3 10 nan Resistance or Tolerance Drought tolerance RZ892 BCD386
Osa10LNT0073500.3 10 nan Physiological trait Sterility C701 C16
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