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

>Osa03LNT0229600.2

AACACTGAAACACACAATAGCGTAATCACCACAAGTACTACAAATCTGGTTCTGAATCATAGTGCTCACTACTGGCGAAAAGCACGCGAAAATTAAACAAGATGGCCTTCAGGTTGGTCTCTCTCAGCTCCTCTTAGCTGCAGCACATTTTTTAAAGCGAACATACTGCTGGCATCCACTACTTATTAATCACTGCTAAATTGCTACTTCTACAGGGATAAAAACATGAAGAAGGAAGGGAAAAGAAAATGCAAGGAAACCAACAGGGGAAGCAAGAGCCGATGGCTACTTGAGATGGCTGAACCAACTGGATGGCTTGCTGAAGTTGCTGAACCAACTTGAGAATCTGAAGTGCCTGAACCAGATTTTGAGCCAGGCCCTGATGCCTGCAGCATGTTCTTGAACCAGTTGGCTGAGTCCTTGGGGTACCGTTTGAGAGTAGTGAAATCAACATAGACAATGCCGAACTTTGATGTGTAACCTGACAGCCACTCGAAGTTATCGAGAAGAGACCATGCGAAGTACGCAACCACATTTGCACCATCGTCGATGGCTTTCTTCAGTTCAGTGAGGTAGTTCTTGTAGAACTCAATCCTTTCGGTGTCATGCAGGAACTCTTCACGAGTGAGATTTCCAGATTGATCCATTCCATTTTCAGATATGATGATTGTTGGATTATTATACTTCTCCTTTATGTAGTTCACAGCTCCATACATGCCAGTCGGAACGATATAAAGCCAATTAGAGTTTGCCTGCTGTCCAATTGGTACGCCATTTCGTTGAAAGATAAATGAAACATGCCAATCAGATGAGTAGCTAGTTGCTGCTTGCTGAGGTGCTGGTTGGTCTGCCATGTAGTTAGCAGTATATTGATTGATCCCAAAATAATCTGCGGAGCCCTTGACTAGCTTAGCTTGTTCAGGCGTGAAAGTAGGTAATCTTTCTTTCACAATATCTCGCATATTTTTTGGATATTGTCCATTTATTAACGGATCAAGAAACCAACCAACATGGAAGTCTCTGGCTCTTTGAGCTGCTGCTTGGTCTTCAGTTGAGTTAGTTAGAGGTTCATACCAATTAAAATCGAGAACTATTCCGATCTTGCCTTTCTGACTTGCCTGGAACTTGTTACGGTATCTATCAACTGCAGTAGCATGAGATAAGATGATATTATGAGCAACAATATATGGCTCTGTTGCTGAGTTCCCACCGGCAGCACACTTGGTGCATCGGTTAGGTGGGTCTGTCCCTGTATCATGGCCAAGTGCTGCTACTATCCTTGGCTCATTAAACGTAAACCAGTTCTTGACTCGATCGCCATATGTCTTGAAACAAAACTCAGCATAGTCCGAAAATACACCAACAATTTTTGGGCTTAACCAGCCTTCATACTTTTTCTGAAGTGCAAGTGGGAGATCGTAGTGGTTCAGATTGACGTAAGGAATAAGCCCTTGCTTAATTACATAATCTATTAGATTATTGTAATATGCCACACCTTCCGTGTTAACTTTTCCCTCTCCATCAGGGAAAATCCTTGACCACGAGATTGAAAACCGATATGCATCGAAATTCAGGCTTTTCAAGAGATCAACATCTTCCTTGTAGCGATGATATTCATCTGTAGTAACATCTGCATTCCCATTTCCCGCAATATTCCGCAGTCGTCATCTGCCGGCGGAGAGCTCGATGGCTTCCTGGTTGAAGATGGAGTCCTCGCCCCAGTCGAAGCGCTGCTGCATCCGCTCGTAGTCCTGCCGCCGCGTCACCTCCACCTGCTGCCACTCCTCCCACCGCTCCGCGAGTCCTTCCCCTTCCAGCATCCGCACCACCTCCGACATGGACGGCCGGTCCTCCGGCGACGCCTGTGTGCACAGCAGCGCGATCTGTATCATCATCTCCACCTCCTGCCCGTCGTAGTTGCTGCTCAGGTTCCGGTCCACGATGGCGCCCAGCTGCCCTTCCCTCTGCAGCTTCTTCACATGGTCAAGCAGTAGCACATCGTCTTCTTCCTCCAACCGTGAGAAGTCGATGGCGCGTTGTCCAGTGACCAGCTCAAGAAGCATTATGCCATAACCAAAAACATCAGTTCTCTCCGATGACTTCCCTGTGGACAGATATTCAGGCGCAATGTGACCCATAGTTCCACGGACTTGAGTTGTCACTGATGTCTTCTGTACATCAACCAACTTTGCCAGGCCAAAGTCACCAACAACTGGCTCAAAATCCTCATCAAGCAGGACGTTGGCAGCCTTGACATCTCGATGTATGATCTTGGGATTACAGTGCTCGTGCAGGTACTCCAGTCCACGTGCTGTGCCTATTGCCACACGTTTCCTTGCTGACCAATCCAATATTGGTTCGCCAGGTTTGAATTCTCGTAAACGATAGGCCACACTAAGATTCTGCATGAAAGGATAAACAAGTAGACGTTCTGTTTGTGTTGTACAGAAGCCAATCAATCTTAAAAGATTCCGGTGAACTGCAACACTGATAAGCTCTACTTCACGCAAGAATGCAGCCTCCCCACCAGGGCTTTCATAATCTGTCAACCGCTTTACAGCAATCTTAGTGCCATCTGGAAGTGCTCCTTTATACACTTTACCGAAACCCCCCTGTCCAAGGACATTTTTCTCACTGAAACTATCGGTTGCAAGTTGTAATTCTCGCCAGGCAAATCTTTTCAACTGACCAAATGCAATTCTTCGATCGTCCTCGCCTGATACATCGACAAAAACTTCTCGTAGATGGCTTTTCCTCCTTCCATTACAGACAATAAACACAGCCCCTATTATAAGTATCCCTATTGCTCCTACAACTGTTCCGAGTACAATGCCTACCTTTGAGCCATGGGATGAACCTTGATAAGAAATACTTGATGAGCATGGATGCAGAAAGTTTGCTCCACAAGTCAAGTTATTACCAGAAAAGTTGTAACGTGCAACTTGAAACAGCGAACCAGGTATTGAACCAGAGAGTTTATTGTAGGCTAACCTACTGCAATCATAAGAAAAAAAATATGTTAGTCAAATAATTCAGGCATGGACTGTTGTCAACAGAAATCATGTATGAGTCCTTGCATGTCTGTCAAGCTTGAGATTCTTGCTACAGTATCAGGTATAGTTCCGTTGAGATTGTTTTGACTTAGTATCAGAATTTGGAGCTTTGAAAGCTGGCCAAGAGAAGCCGGTATTGGTCCAACCAACAAATTGTCTTCCAAATCCAAACTTGTCAAACTAGATAGGTTGCCGATCTGCTCAGGTATGCCACCAGTAATCTTATTACCAGGCAAGGACAAAACATTCAAAAACTGAAGCTCTCCAATTCGTGGTGATAGAACTCCAGTGAATCCCATAGATGCCAATGTTACTTGCACAACATTGTAGTTGTTGTCACAAATAACAGAATTCCAAGTGCATGGGTTAACTTGATTTTGGTTCCAGTCAGAAAGCTGGTTACCAGTAGCATTCAGCTTCAGCTTCATATCATATAGTGCATCACCTTGACGGTCAGATGCTGAAAATGGGAGCAGAGATGCTATAATTAGGAGGACGCTGAGCAGATCCATGACTCTTCAGTTATAATTACAGCATCAAAAGAGTTCCTTGGGGAAACTTGCCCGGCGAAAAAAAGTACACGAACTGATCATAGTAGTATAATACCGGAGTCCCTGGCTAACCCAGTTAACAAGCAAGCCAGTCCAGTATGGCACCAGTGGCTTGCCCTCGCAGGCTGGGCAGCAAGCAGGTCGTCGCAGGTCCACGCCGCCTCTCCCACTTCACCTCCTCACCCCGCCGCCGCCGCCGCCGCCGCTGGCGCGCGGGTAAAAGGCGTGGGTGGGGCGCTGCGCTGGAGCAGTTGACTCGAGGAAGCAGCAGGAATTGACCGGTGCTGCCGGGGCGGAGCGCGTGCGGCCATTTTTTTTAGGCGCGACGCAACTTGGTTGGTTAGGTGGATCCCCCTCCTTTTTACCTCCCCATCTCTGGATAAGACGGAATTCGGCGACCTTCTCCTCCGGATCGCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.993275
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0229600.2 3 28252248 A G
Osa03LNT0229600.2 3 28248851 G A
Osa03LNT0229600.2 3 28249094 G C
Osa03LNT0229600.2 3 28250884 G C
Osa03LNT0229600.2 3 28251016 T C
Osa03LNT0229600.2 3 28251160 A G
Osa03LNT0229600.2 3 28251750 A T
Osa03LNT0229600.2 3 28252107 A T
Osa03LNT0229600.2 3 28252756 T G
Osa03LNT0229600.2 3 28252876 C T
Osa03LNT0229600.2 3 28252897 T C
Osa03LNT0229600.2 3 28253049 C T
Osa03LNT0229600.2 3 28253280 G A
Osa03LNT0229600.2 3 28253439 G T
Osa03LNT0229600.2 3 28254355 T C
Osa03LNT0229600.2 3 28255270 A G
Osa03LNT0229600.2 3 28255767 A G
Osa03LNT0229600.2 3 28255794 A G
Osa03LNT0229600.2 3 28256377 T C
Osa03LNT0229600.2 3 28256430 C A
Osa03LNT0229600.2 3 28256795 G C
Osa03LNT0229600.2 3 28258007 T C
Osa03LNT0229600.2 3 28258189 T C
Osa03LNT0229600.2 3 28258539 G A
Osa03LNT0229600.2 3 28258698 T C
Osa03LNT0229600.2 3 28258761 C T
Osa03LNT0229600.2 3 28255045 A G
Osa03LNT0229600.2 3 28250728 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0229600.2 osa-miR5790 Translation 4.5 11.307 1 24
Osa03LNT0229600.2 osa-miR5814 Translation 5.0 15.351 1 24
Osa03LNT0229600.2 osa-miR5816 Translation 4.0 11.802 1 24
Osa03LNT0229600.2 osa-miR160a-3p Cleavage 4.5 20.751 1 21
Osa03LNT0229600.2 osa-miR160b-3p Cleavage 4.5 20.751 1 21
Osa03LNT0229600.2 osa-miR160d-3p Cleavage 5.0 20.751 1 21
Osa03LNT0229600.2 osa-miR395c Translation 3.5 13.145 1 21
Osa03LNT0229600.2 osa-miR166k-5p Translation 4.5 13.659 1 21
Osa03LNT0229600.2 osa-miR1861c Cleavage 5.0 19.316 1 22
Osa03LNT0229600.2 osa-miR1863a Cleavage 5.0 16.406 1 24
Osa03LNT0229600.2 osa-miR2926 Cleavage 2.5 20.981 1 20
Osa03LNT0229600.2 osa-miR2928 Translation 4.5 18.206 1 20
Osa03LNT0229600.2 osa-miR395x Translation 3.5 13.145 1 21
Osa03LNT0229600.2 osa-miR812o-5p Translation 4.5 20.35 1 21
Osa03LNT0229600.2 osa-miR5149 Cleavage 4.5 20.461 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0229600.2 3 Qpn3 Morphological trait Culm/leaf CDO337 OSR31
Osa03LNT0229600.2 3 nan Resistance or Tolerance Blast resistance RM16 RM168
Osa03LNT0229600.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0229600.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0229600.2 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0229600.2 3 qRFWd3-2 Resistance or Tolerance Other soil stress tolerance C944 C746
Osa03LNT0229600.2 3 Yd3-13 Morphological trait Seed RZ403 CDO337
Osa03LNT0229600.2 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0229600.2 3 qRFWw3 Resistance or Tolerance Other soil stress tolerance C944 C746
Osa03LNT0229600.2 3 nan Resistance or Tolerance Drought tolerance C746 RZ448
Osa03LNT0229600.2 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0229600.2 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0229600.2 3 nan Morphological trait Panicle/flower RZ448 RZ403
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