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

>Osa03LNT0233700.4

AAACCAAACTGGCGCCTAGTATTGTCTGCAAATTAACTCTTTAAAAAGAAGGGTAAACACTAACGTCGATATGTGCAAAGCCAACCAAGTTTCGTCACCAGAAGCTTTAACGGTAAAGAAAGCTTTTATTCCTAAAAGTTGGGAAGTTCTAAAGGAACTTTTGCTCAAAGGGTATGAAACAGAAAATGAAACCTTCACCATTTTACTCTAATTACAAGGGCTAAGCAGGCATTCCCGCTTTTGTTCTGCAGCCTCCCCTCTGCAGATCGGCATGGTCTAGCTATGAGTTTTCTCTGTCCCTATGAGTTAGGCAATGGTATTGTGCCCTCAGCATAAACAAAAGTTTCTTCCTCCCGATGAAAGAAGGTTCTTGAGCAGGAGGTATCAAGAAATGTTTCCCCTAACAGTTTGGGACGAAGATGGGATAGCTGGCTTCTTCTCTATTTGGTCATAATGAAGAACAAAATTGTCCTTGCGGATTGTCTCCCAGTTGTTTGGATCAAAGCAACCGTAAGACCCTCGTTCATAATGAGGAGTTTTGACCAGAGGCTCAACATTTGGAATTCTTGTGAGCCACACTCGCACTTCTTTATGATAAAACCATCCTCGGTTGTAAAGCTCACTAGCAGCACATAGCTGAGCTTCATCCCTTGGCATGCTATAGAAGATGTAAAACAGCGTTAACGTCTGGAACTTCTGAAAATGTATAGGTTGTAGCGGTGGAGGTTGCTCAGCATTGTAGCAAGCTGGAATATGAAACTCAGGTTCTCCTTTTGCTGGCTCATTTGACCATGGAGAACCAAATGTCTTGTATAGATTGTCTGGTGAGTTCAAGTTTAAACCCAATGTTGTCAAATCCATTCCTAAAGCAAGAGATGCTAAGTCAGCATCATTCATCCTGATAACTCCCAGCAATCCCATCAAACCATAAGGATCAGGTGGTGTTTGCCCTCCCTGGATGGACTTTAGACTTTGATCTCTGTATGACTGTGTAGCTGAAGACACCTGCTGCAATCTGAAAGGATTTTGAGTTTGAGGCTGCTGGTATTGTTGGATAAGTTGCTCGTATGATCCCAAACTAGAAGTTTGACTTGCAGAAGATCTTAATCCGATATTTTGGGGACCAGCATTCTGAACTGAATTAGCACCTTGCTGGTGTTGCTGACGATTTGGTGGGTAGTTACTTCCTAAATTAAAGCCAACTGACCTTGACATCGGATATTGCTGTGCTTGCATAACAGGCACATTATCATGAAGTTGTTCCTTGTGATGCAACTCCATAGCATAATCTGAAGTGCTACCTTTGTATCCAGGTAAAGCTGGGAAGTCTTCATTTTGAATGCTAAATTCCTGGTTTTGTTGAACAATGGTGTTAACACCAACTCCTTGCTTCCGCAGTGAGCCTGCATATTGTCCTTGCGGACCACCAGCAGAACTAGGTCGACCAGTCAATTGGGGAAAATCATTCATGTCATATGGAGCACTGTCATTGGCATCATGCAGCATCCCCATGGAACCAAGGGAATTATTTCCTCCTTGTATTTGGTTCTGAGATAATGAACCTCCAGACGTCGGATATGAACTCCCCATCATGTTCATCATTTGAGGCGATCCTGATCTCAGAGATTAAAAATAAAAGGCTGAATGCAAAGACTCACAGGCTTTCACTTCAATAGATATAAACTGATATACAATATACCACTTGTTAAACAGTAAAATATTACAGAGACATTACATCACAACCATAAACAAAATTAACAATTATCAAATTAAGCAATTAATATTCTGGTATCCGATGCATGCATGCAAAAAAAAAGGAGGAATACCAATATTATCTCTAACTTTGACACGTATCAAATGCTAGTATTGTTGGTATTTTCATTAATAATCTTAATTTTATCAAATGCAACCGATATAGGTTGGTGTTCTATTAGGACGCAGTGTCGCAGTGGAGTAGTGGACACTAAGATTGCCCAGCTGAATGTATTAGCTTTGGGTGTTATAATCACATTATAAAGGCAGTTATTGCAAGTAACTTGCCCAGGTAAGGGAACATGAAAGATAAGATAAAGCATAAGCCATACTGTGTTTGATAACAGAGTGAAAGCACCAATTACTCCAGCAGATAGGTTGTGGTCAGTGCTTCATCAAGCTGAATTTCACTTGAGGTATTGGTCATTTAGAGGAAGCTTGTTCAGGCACTAGGTTTCTTGTTTCTGATTATAATCGCACTTACCAAAACTTTTTAGTTGGCTAGTAACAGCACAGGAATCCTACTCAAGGAAGACTATTGGCAGCTACTAAGAATGTTAATTAAAAATTCATTAAATACCTATCATTTGGGTATTTCCGAGGACTTGTTTCATATGCCCAACTCTGATGTCAAGAAAAAGAGGGCTAAGTTTGCAGCTAAAAGCAAACAATATAGTAAGTAGATATACTCAACAAAAAATCAGCATTGCGATGGAAGAGCATTTCTTAACAAACAATAGTTGACGATAAAAATAACAAGAATAGAGAAACAAGTATGCAGCCATGAAAGCATGACCACATAAAGAGTATTAAACTCTACGGAGTACTCCCTCCATTCCAAAATGTAGCGATTTCTGGCTACGAATCTGGACCGGGTCCTTGCTGAAGAATGCCATTCATCATCCTGCTGGATCCTTGGACATTTAGACCGCCACTGCCAATATTGCCACTCAAATTCATGCGTGATGCTATGCTTGGCACAGATAATCCACCAGAGCTTATATTCCTTCCAATGTTACTTCCACCCACAATATTTCCTACAGAACCAGTGATCCTAGGGCCCAAATTTCCCAAAGCTGGAGATACTGACATCCCAGGAACAGAATTCCGATTACCACCAGCACCCAAGTTTGAGGATAAGCCTTGAATGGTACCTCCAATATTCAAGCTACTACTAAATGCTGGACCTCCGCCAACATTCACTCTAGAACTGACTCCTGAATGCCCATGAGGAAGCTGAGACATTCCAACTGGAAGGTTGTTTGAAGCAAATCTTGCAGAAATGCTCCCTCCAGGCTGTTGAACCCCAGAGGATGGAAGGCCACTCATGGCAGCATTCCTCTGAGCAAGCGATCCAGGCATATTTGGCAGATTAAAATTTGCATGGATGTTGTGCAAGCCAGAGTGATGGAACGCCCCTGGAACTGATCCAGATTGACCAGAAAAGGATGCTGTAAACGGTCTTCCAGATGAGTCTTGAAGGTTTGATGCAGAATTGTTCAGGTTTGACGAGAGAGTCCGCCCGCGCCTGCGGCACGGGCAGCGGCGGAGAGCGGGGAGGAAGGGGCGGCGCGCGACGGAGGATTCGGCTGCTCGGGGGTGCGATGTGAGGAGGAGGCGATGGGTGCGCGGCGGCGGCGGCGGCGGCTGCGTCTCGGACACTCGGCGATTGTGTGGGAGGGCAAGGGGACGGAAATAGTGCGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.946729
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0233700.4 3 30159145 C A
Osa03LNT0233700.4 3 30157878 T A
Osa03LNT0233700.4 3 30158963 A G
Osa03LNT0233700.4 3 30159046 C G
Osa03LNT0233700.4 3 30161460 A G
Osa03LNT0233700.4 3 30166275 C T
Osa03LNT0233700.4 3 30166285 G A
Osa03LNT0233700.4 3 30166597 T A
Osa03LNT0233700.4 3 30168419 A G
Osa03LNT0233700.4 3 30168829 A T
Osa03LNT0233700.4 3 30169022 T G
Osa03LNT0233700.4 3 30169486 T C
Osa03LNT0233700.4 3 30171019 C A
Osa03LNT0233700.4 3 30171163 T G
Osa03LNT0233700.4 3 30171272 A T
Osa03LNT0233700.4 3 30157661 C 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
Osa03LNT0233700.4 osa-miR6248 Cleavage 5.0 21.697 1 21
Osa03LNT0233700.4 osa-miR395f Translation 4.0 22.401 1 21
Osa03LNT0233700.4 osa-miR396a-3p Cleavage 5.0 19.18 1 20
Osa03LNT0233700.4 osa-miR396b-3p Cleavage 5.0 19.18 1 20
Osa03LNT0233700.4 osa-miR319a-5p Cleavage 4.0 18.482 1 21
Osa03LNT0233700.4 osa-miR167d-3p Cleavage 4.0 20.163 1 22
Osa03LNT0233700.4 osa-miR443 Cleavage 5.0 19.022 1 22
Osa03LNT0233700.4 osa-miR169r-3p Translation 5.0 17.037 1 21
Osa03LNT0233700.4 osa-miR1435 Cleavage 4.5 16.845 1 20
Osa03LNT0233700.4 osa-miR1436 Cleavage 3.0 21.641 1 21
Osa03LNT0233700.4 osa-miR1439 Translation 2.0 20.679 1 21
Osa03LNT0233700.4 osa-miR1846d-5p Cleavage 4.5 20.895 1 22
Osa03LNT0233700.4 osa-miR2097-3p Cleavage 4.0 22.194 1 22
Osa03LNT0233700.4 osa-miR2105 Cleavage 4.5 17.097 1 20
Osa03LNT0233700.4 osa-miR2105 Translation 4.5 7.93 1 20
Osa03LNT0233700.4 osa-miR2877 Cleavage 5.0 23.226 1 24
Osa03LNT0233700.4 osa-miR5340 Cleavage 4.5 17.097 1 23
Osa03LNT0233700.4 osa-miR5506 Cleavage 4.0 20.144 1 21
Osa03LNT0233700.4 osa-miR2873c Cleavage 4.0 23.465 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0233700.4 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0233700.4 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0233700.4 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
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