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

>Osa03LNT0224700.2

GTATATGCACAAACTTCAAATCAAAATCACAAGCAACCATACAATTCTGAGAGATTGTTTGCTTCCTATTTCTATATGACTCTTGCTCATCCAATGGAAGTTTCATAGGGATATGAGTACCATCTATAGCACCAATACAATTCTGAAAAAAGGGGTAAAATTGTGGTTTCCTCAAGATTGGATGTGGGTGTAGGGATGGTGCACGAATGTAGACAGATGTGAGATTTGTGATTGCTTCCTGCACTGCTTTGAAATATCTATGTATTGTGTCTGGACTATGCTGAAACCAATCTTGAAGTGTTTCATTGGTTGCATTTTTTGCCACTGTATATAAGAATATAGCAATATGCTCTTCTACTGAAACATATAGTACCAGTTAGGTACTCTTTCTCACGTAACTTATTGACTAGTGCATGAAAAATGTCGACCTCCATACGGAAGTTTCTTTTGCATAATCTTTCATGTCCTGTTAAAATCTCATGTACACGGCAACCCCCTGTAAGTTTTGACGTGTGCATTGGTCTCCTAATACAAGATGATTGTGATGAATCTCCTAAAGTAGGCAGAACAAAATGAATGAACTCATCATCACTTTCTGATATACGTCGGTAGCTTGGATTCATGGTGTGCAGATGTTACCAAACTGATGCTTGTTGTTACACGAGCAAGTAACGTCCAGCTATGGTGGCTAGACGATGAGTAAAGCTTCTTGCATGATGACCCTACTGGATGCCCTTGCTCAATTTCCAGATTAAGCTTTGTCACATGCTCATTTTTCTAGACCCACCCTGCAATCACATGCCAACAAGAACAACAAGACACTGAATCTAGAGATAATTGACCAAACCCAGAAAGTGGTATATCACAAACCAGACAAGTCAACTTCTTAAGAAAATATCCACGTCACCATGGACAAAAGATAGAATCTGCAAGCAGAGTAAGGCATAAGCAACACAAAATGAAATACAGACACAAGAACAAGAGATGCAAGGCAAGAGAGCACTAAATAGTATATAGTTGTATTGGCTTGAAGCTCCAAAACACACCCTCGAACCCTCCCGTCTTTGTGGGCATTGAATTTTCAACAAGGAGTTGAAGGGAAAATGCTAGTGGTTCAGAAAATTTCAATCGGAGTTGGATTGCCCTTCCAAAATGACCGAAAATGGACCTGAAACGAGCAAAATACTATCTTCTCTGAATCTTTATTTAGGTGGAAGCTGCTTAAACATCAGAAAAATTATGTCATGGTGGGTGAGGGATAAGCCTGGCTTTAGAGAGGTCAAAGAACATCCAAATCCGTATTGATTTTGCACTGCAACTCTGAATGTCGTATCTGCAACTCCAACAAGCCAGTACTTCCAATTGCTGGACAAAAAAAGCGAATATCCATGTAAGCATCGCTTAAACTGGACTGCAAGAACTGAAAGCAAATGAGTTGATGAGTATATTGCGGCTTCATGGTCTTTTTTCCAGTTATGTGATCGTTGCTCCAGTCAAGCTTCAACCTTTAACTTGCACATATCTGAGCAGCAACAAATCCAATCAGGGTTGTCATAGCTATTGCAGCACAAACTTCGTAATATCACCATAGAATCAAAAATCCTTCTGCATCATCTAAACAAGAACAGAACTCATACCACAAAAAGAACCAACTCAGGTTGTCTTGAATCCACTCAAACTAGGGGATAATCCAACAACTACCCATCAGGGAAGACCACATAAGAAGGCCAAGCCAAACGATCCGTATTCTGAAATCGCTAAATCCAGATAACATAATCTCAAAAAATCAACCAAAACCTTGTATGCCCCTTCGTTGACATACAGAGCTCCAATTCCCAGACCGACCCTATGACTATCATGCGAACAAACAGCTCAGGCATTGAACTTATACTTAATGATTGAGGTACAGTGATAGAACACAAACCGAACAAGTCAACAGCCTCCAATCAATAACCTTGGAGAAAATTAAAGAATCTGTGACAAACAAAGAAAAGCAAAGGCACACCAAAATCATAGCTATATGTCGTAGAGAGCAATTCTGATGACCGAAACAGAAATTGAACGAGAAGGGAAAAGTTTTAGGCAGACTAGCAAAAGTATGTTCTGGTTGTAGGATTCTCCTGTAGTCCCATCTATCTTGAAGCTCCATAACTCCTATGCAATTCCATCTCTGCAGGTAAATCCGAGTATTTAAATTCTACCTTTGTGAGAATTTAAGGGTAGTGATTTAAAACTCAGAATCAGGTTGGCCTTGCAAATTTATGAACTTGACCTGCAGTGAGCAAGAGACCATTTATTCGGGAAGAAATTCAACTTTGTAAATATTTAATTTCTAAGTGATGAATTGAAGAGAAGGTGATTTAAAGATTTCACTCAGCATCAGAATGGCCTTGTAAAATTATGAACTAGACCTGCAGTAAGCAAAGAGACCATTTATTTGGGAAGAAATTCAACTTTGTAAGCATTGAACATCTACTAATGATTAAGAAGGGAAAAGGGTGGTGATTTAAGGCTTCACTCAGATAGGCCATAAAAATTATGTGGAGCCTTGCAATGACCAGGAGACTTTATTTTGGAGGAAAGCAGTCTAAGCATAAACAAAATCACTTAAAGACTGAGTGGCATAAAGTCTGGAGTTTGCAGATATTAGTATAGACCGAGGCAGATATTGCAAATTCCATCTTTGGCATAGGAGTATCTGCAAGAACTATTAATTACTGACGAAGAACATGTAAAAGAAATCAACTTGGTTATCAAAGATTAAGCAGGTAAAGGTTGTCGATCACAAAAAAGGGACTGCTAGCAGCCTGTATAATTCCAACTGATGCGGCAAATAGGACTCGCTGTGAGCTGCATATATCCAATTCCTGAAGAACAACCAACTTCCCAAATCAGACCTTCCAGACATAAATCAAATTATGCTGACAACTAAATAAAATCAAGGGGGATCAGGACCCAAAAAAACATTGAAATGATGAAATCCCCATCTAACAATCTCCCGTATAATCTATCTCCAAACCACTTAGAAATCTGCCCATCTTGCGGATCTGACCAAAGGAAATCCAGCCAGGATAGTTTCAGAACTTCCATGTCAGGATAATTTCAGAACAACCGTGCACTAATCAAAACAACCAAGAACCATAATTCATCATGAATCCAAAACAACCATGAACCTGGACAATAACAATCAAACCTCCACCAATCCGGTTCATCTCAACAGTCATCCTCCCTCCTGCATCATCTAGAGGAGCACAAACACATACCGACAACAAGCCAGATCAGCGGTCACAAATAACAACAATCAACCCAGGGTCTCGAATCACCTCGCGTGAGGAATGATAAGAACCGATGATCATCCATCCATAGATTGAAGTAACGTTAGCATATCCACTCAAATTGCCAAATCTGAAATCACCGAAACCAAGTGACTAAATCAAACGGACCGTAGACAAGAAACGTTCACCTCTTCAACCACACGACGCCACAGGAACCTCCAATCCTGGATCAAACCCGCTCCTGCAACCGAACACGCCTAGAGGAGGAAACACGGGGAAAAGGTAGAACACAGAATTCAAAACCAGAACAAGATCGGATCTAATCGGAATCAAATCACCATAGAGAGAGAAAAAAAATCAAACACGTCGCAAAGCGAACCGAACAGGAGGGGCTCCCGGAATCGAGCGTAGACGGGGCTCATCTCATCTCATCTCACCGGCGGTGATCTGCGGGAACAGAAGGCGGAAACAACAACGAGGACGATCCAAATCAACCCGACGATTCAGAAAAAAAAAGGAAAAATAAAAAACACAACTCGAGTCGAATCGAGAGAGGAGATCGGAAACGGGAAGAAGCAAAACGCGACCACACGCCCCCGGTGAGAGCACGAAGAAGAAGACC

Coding Potentia
Explanation CPC Score
noncoding -1.33993
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0224700.2 3 23627898 A G
Osa03LNT0224700.2 3 23624435 T A
Osa03LNT0224700.2 3 23625095 A G
Osa03LNT0224700.2 3 23625559 T C
Osa03LNT0224700.2 3 23626679 G A
Osa03LNT0224700.2 3 23626879 T C
Osa03LNT0224700.2 3 23628147 T C
Osa03LNT0224700.2 3 23629963 A C
Osa03LNT0224700.2 3 23629997 T C
Osa03LNT0224700.2 3 23627827 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0224700.2 osa-miR5537 Cleavage 5.0 16.548 1 22
Osa03LNT0224700.2 osa-miR5820 Translation 5.0 20.716 1 21
Osa03LNT0224700.2 osa-miR6254 Translation 4.5 19.457 1 21
Osa03LNT0224700.2 osa-miR7692-3p Translation 4.5 14.172 1 24
Osa03LNT0224700.2 osa-miR319a-3p Translation 5.0 7.805 1 21
Osa03LNT0224700.2 osa-miR1429-5p Translation 4.5 13.97 1 21
Osa03LNT0224700.2 osa-miR2055 Cleavage 4.5 11.939 1 21
Osa03LNT0224700.2 osa-miR2093-5p Cleavage 4.5 12.623 1 20
Osa03LNT0224700.2 osa-miR2871a-3p Translation 4.5 6.276 1 21
Osa03LNT0224700.2 osa-miR2871b Translation 4.5 6.276 1 21
Osa03LNT0224700.2 osa-miR2872 Cleavage 5.0 14.633 1 21
Osa03LNT0224700.2 osa-miR5515 Cleavage 5.0 11.214 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0224700.2 3 ccf3b Physiological trait Source activity RM16 RM282
Osa03LNT0224700.2 3 ccfs3 Physiological trait Source activity RM16 RM282
Osa03LNT0224700.2 3 nan Morphological trait Panicle/flower RZ403 RZ452
Osa03LNT0224700.2 3 nan Morphological trait Shoot/Seedling RZ284 RZ403
Osa03LNT0224700.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0224700.2 3 An5(t) Morphological trait Panicle/flower C1677 R19
Osa03LNT0224700.2 3 gw3.1 Morphological trait Seed RZ672 RZ474
Osa03LNT0224700.2 3 nan Resistance or Tolerance Insect resistance G332 R19
Osa03LNT0224700.2 3 qGL-3 Morphological trait Seed R19 C1677
Osa03LNT0224700.2 3 qLWR-3 Morphological trait Seed R19 C1677
Osa03LNT0224700.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0224700.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
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