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

>Osa04LNT0271600.2

GAGAATTCACACCTAGCAATTCCAACGGAAATCATACAGCAAATGAAAATGGGGCAGACACTAGGTCTCTCCATGAACCTACACTATCCTTTTTCTTTGTACAGTGTAAGCACTAAGTGGTACAAAAGGAAAACACTCATTAACACTCACCATGCTGACAAAAAGAAGAGGTTGAAAAAAAAAAGGAATACATAATCACACAAAGAGAAAAAGAAGGGCAGGAGCTCGATACACAAGGGGCTTTGTTTATACTATACACATGCACAAACAAATGAAACCCAAAAATGCACCCCTGCCAAACAGGTATTCATACAGAACACAAATAATAACAGGGCGTTGTGTTGCACCTCAGGTCATTGGTTAGCATCAATCGGAGCGCCAGACCTTGCTTGTGAAATCCGGTTTGCGTAGATAGTTACAAGGCGCAGCTGCGTGCTGTTAAGCCCTTCCAAATACGGGACGAATGCCTTCCCAAGCATGATGTAGATATCCACCAAGCAGAATACAACAGTCTTTCGAACATCAGGGCTTTGGTTACTAAAAGCATCAAACAGTGCTGGCAAAAATGTGGGCAACTGATTCATCAATTCCTCCTCGGAAAGCCGTCCAACAAGCTGCAAGATTATCCAAACAGAACCAGCAGTCAACAACACTTGCTAAAATTATATTTGGTTTACCGGTTTTTAATCAGTCGGAGACACAATGCCTAGATGCTAGAGGTGTGCCAATCCAATTGTTTTATTCAAATACATATGATTCATGTGTCCTATGCAGGGCATACATTTACGAACACACGATTAGTTTATTGGCCGCATTCTTCCGCACAAAGTAGTAGAATGGCGTATATACTCAAACAACAGGTTGAAGAATTCAAGAAAGGGGCATCTACAAGACTACAACCCACTAAATTGTAACATTGAACGCTAAAGCAATTCAGATATGTTGCAATCTGACCACTTACCAGAGTACCCCCCCAAAAAAATCATAATATATACATGGAACTGAGAAAAAAGCACTTGCACAAGAGATCAGGAAATCTAACCAAAGGATGTGTAATACGTTAGGTTTGGTGGAGCAAAATAACTGATAGGACAACTCAGCAGAGAGTAATTATATTATCAATTGATGCTATTTACAAAAGATCAGATATATAAAGAACATATGATATGAACTTATTCACTAAAGAACCATGGCACCATGAAGTTTATATGTTATATTGTTATTATGTGCCATTCAAACTTAAATGGGAAACGCTCAAACAGTAAACAGGGAAAAACTGCAGGTACGAGACACCTTTGTCAAGGAGTTGATACACACAACAAGTGTCTTTTCATCATCACTGACCAATAGAGGCACCACAACAGCAAGACATCTGAAAGGATCATATTTTGCTAACAGAACATTTAAGCACTGGTTTGCCTCATTTGAAATCTTTGCCACCATGTCTTTGGTAACATGCAGAAGTTTCTCCAGAACAATTTCAATAGATTCTTCCATAGCACCACTCTGATTGTTGAGCATCTCGGCAACTAAAGACAGAGCAATCTCCCTAGTAGATGAATCAGAATCATCCAGCACCTCAAGCACAGCCGTTAAGATTTGATTGAAATACTTTGCCCAAATGGAGATGTCATTATCAACAGAAGCTTTAACCAACTGCTGTAATGCTTCCCGCTTTTCCAAACTTGAAACTTCGGTACCGTTGCTTATCTGATGAAGAAGTTGTGGTATGCTCAGTTCGTTGTCAGCATGTAGGGTAGTCTTTATAGAACTAAGTTTCACAGCAATATCTCCCTCTTGAACATTTTCTTCAGCAGTAGAACCAACAGCATTGTGCCCATCAGAAGCAGCGCGATGGCTTAAGTCTAAGCGAGGAGTACTGATAGCAGTTTCATCATCCAAAGGCGCATCAGTTTTTTCAGGATAGTTTGGCCAAGAACGAGCAGTTTCCACTAGTGAGCTAGTATTATTCTTTGATTCTCTACTTCTAGTTAAAAGAACTTCACTTCCAGTGTCCAGTTCTATGCTTTGACTAGTATGATCTATGCTCATATCAGAAGTAGTTCTCGCCATAGGCGCATTACGCGGTGTTGACTCTTGCACTGAATTCATCCATTTCCCACCTTCAGCATCAAGGGAACTAGAGGAATACCGCCCAAATGGATAGCTTTTCTTTGATGCAAGCGCGTAACCATCTTCGGAAGAAGTTCCATAATCTGCTTGATCATAAGATTTGGGACGGGGACGATCTTTCTTGCTCTGTAAGTAGTTCACTAAATCAACTTCAATGCGAGGTGTGTATTGCTTCAGTGCACGCCTCAAGAGGTTTTGCTCCTCAACAGATAAGTTTAGAATAAAATTTAGCACTGCTGTTGAATCAAAATGAGAATAAACAGATATGATACCAGAAATGGATGCCTCCTTCAGTTTTGCATTTTTTTCATGAACTAAAGGTGCCAATTTTGAAAGCCACAGTTTAAGGAACCCACTGTTACTATAACCTTCAGAATCTACAGTGTACTTGCTGAACGATTTATTTGCGAACTCAAGAACAGCCAACTTTGCCTTTGGGGACCTCTGTTCATCTAGTGAGCGCACTAGGGCAGGTAGCAACATATCAATTGCATATGTTCTCCCAACAACATCCAAGGTTGATGAGCATGGTTTTTTTACCAATTCTTTTGGATCAATAAGCCGGGAAAAAACATATGGCAAAATTCTTTCAACATAACTCTCAAATGGCTTCTTGCAAGCTGGAATAAGTTCTGCAAGAGTAGAAAAGGCTGCTTGTGCAACCTTATGATGAGGGTCATCCAAATGACGAAAAAACAGCTTCATGACCTTTTCAAAATTCTGTGTAATTTCCTGAATACCTCTCTGGCCTTGTTGCAGAAGATTCCGAATAAATTCAAAAGCTGAGACTCTCACTACCCAATCCGAACTAGGGCTGAGACCCTCAGAAAGAGCATCACTTAGTGAAGCCAGTGCATCCGTATAACCAGACACGTCACCTGACTGTACTTGGCTATCGTCAAAGCTGTGCCTGATGCTGGCAGAAGCCCTTGACATTACTTGCTTCCTTAGAAGAGGTCTCTGGAAATTTGGAACATGATTATTATGTGAATCTCTGTGGATGGCATCTCTGTAGGGCATGTCAACATAGTTTTGAGTTTGGGGGAATCTCCTAGTTGACCGGATATCACTACCCTCATCCATGCGGCCTCCTTCTTGTGGCCTCTCCAAAGACCTTCTTGGAAAAGGCAGTGATAAGCTTGTCATGGACTCAGATGATATATTACCCAAGTACGGTGATCTTGATCGCTCTCTGGTGCCCAACTGGGTTGTCATTGACTCCAATAAGCGGGAGCCTCCATTTCGTGCACTAGCATTTATGGTGCTAGGAACAGATGAGTCGAGCAGTGCTGAATTCTGTAAGGACAGATGATTTGAAGCTGTTGCTGCAAGCGGAACAGGAGGATCACGAGACGATGGAGGATCAACCCCTGCACAAGATCCAAGCTGGTTGAGCGGGTAGCTGAGATATTTTGCCTATCTGATATGCTTACACCTTTCAGCAAACTTTCAATGGCAGAAACCTTTTCTTTGCTTGAGTTAAGCACACTCTCTAGGCTTCTTTCAGAACTTCTCCCAACAGTCTTTGACTGTGACAAACGAAGAGTATTTGATGAAAAGGATGAATCTGAAGAAATAGCAGCAGTTTTGTCCATAGCAACAATAGCTGAAGTGCCATATCCAAGTGCACTTGTACCACTTGCATGTGATAAAGAACGAGAAGGCTGCACAACCCTCTCACGAAGAGAGGGTGAAGCATACCGCTTGTGCACACCCCCATCTTCATCGTTTATAGTCCTCTGTATAGCAGGATCAAATGACATAAAAAGCCGACGTGAACGCTCAGGCCATGTCTTTGCAAACAGTCTATAACAACTTCTAGCAGTTGCACGGACCTCACTCATCGCATCTGCTACACAGCACTTTATTAGATCTTCGTATAAATCAGCTGAACGTTGTATCTCCGGGGCATCAGCCCAATACTCCAGTATTAAAAGAGCGTACTCGCAGCACCTAGCACGGAGAACTGCACTTCGGTCATTCTTTGCTGTGTCAGCTATGCGAGGAAGAATTCGTGAAATCTTGCAGTTCCGTAGAATGGTTTTTATGCATGTATCGGCTGATTCAGCTATGACAAGCACTGTTATGACAACAAGCTTAAAAAGCATCGGAATAAATAGTTCAGCACATGGCTCAAAATCACCAAGGAGTTCTTTGGATAGTACATTGAGTAGATGGCATGCCTGTTTTACAATGCTAGACCGTCGATCAGACAGCTGAGTTGATAGAGGTGGAACCAACTGCTTCAAGAGCATAAGAAAAGATGGATAATCAATAGCACCTCCATACACCAAAGCTTCAATCCTTTGCATGGCAGCAATACGCACGGACCAGTCCTTTTCTGGAACAAGGGTAGCTGCAATCTTCTCAAACTCCCGAAGTAATTCTTTCTCTGAGTGAACTCTTACTGGTTCCACTGGTTTTTCTGTTATATCCGTGTCCCCTCCGAATAATGTACTTTCCCGTGGTGTGCTTTTTGTCCTTGGACTGCCTCTTTTCGGATTAACACTAACAGATCTAGATTCGACAGCCTTATATTGCATGATATTACCATCAGATGTGGGAACCTTTGGTTCTATTCTTTCCAATCTTGAATTTATCTCCCTTAGCATGTACGGAGGTAAGTTATGGCGCTGCAACTCTTCATGGAACTGAGATCCCATATGTGTGTACATCTCCTCAATGCAATAGATAGCAGCATCTCGAACACTTTGATTTGAATCATTCATCAATTGCAAGACAGGTGAAAGAAGAACTCGTTGCAATGGGAGCTCGGTTGAAGCAAAAAGCCCAACCGCGGTTGCCACTGTACGTACAAACTCTTCCCGGACCCTCCAACTCTTGTGAGTCCATGCATAACTTCCAGCTCTTTCAACTATGATTGTCGGCGAAGAAACCTCCATGAGGGTGATGAGGAGCTGCCGGGCGGCCTCGCGGACGGGCTGCTTGCCGTCCCCGAGGCGCTCGACGGCGGCCGGGACGAGCGCGTTCAGGTGGATCTTAAAGTGGTCCCCGGCGACGACGGCGGCGGCGGAGAGCGCCTGCAGGCCGCCCTGCGCGACCCGGAAGTTGGCGTCCCGTATCAGATCCATGCAGGTGTCCACCAGCGCCGTCACCTCCCCCGCCGTCAGCCCGCGCTGCCGCGCCGCCGCGTCCAGCGCCTCGTGCAGCCGCTCCACCCCGGCCAGCCGCTCCTTCGTGTCCTTGGCGCGCGCCGCCTCCAGCGCCGCCTCCATTTCCCCCCCGCCCCCACCCACTACACCCCGAGCGACCAAACCTAGGGTTTCGAGCCCGGAGGCGAGCGGCGAGGCGAGTCGAGGAGGGGGAGGGGAGGGGAGTGGCCGGATCTGGAGGAAGGAGAAGGGGAGTGTAAGCGCAGCGAGAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.843507
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0271600.2 4 25352236 G A
Osa04LNT0271600.2 4 25350739 C G
Osa04LNT0271600.2 4 25352303 A G
Osa04LNT0271600.2 4 25354465 T C
Osa04LNT0271600.2 4 25356002 G A
Osa04LNT0271600.2 4 25356568 C T
Osa04LNT0271600.2 4 25357707 G A
Osa04LNT0271600.2 4 25358313 G C
Osa04LNT0271600.2 4 25360158 C A
Osa04LNT0271600.2 4 25359318 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
Osa04LNT0271600.2 osa-miR5539a Translation 4.5 14.406 1 22
Osa04LNT0271600.2 osa-miR5807 Cleavage 5.0 17.989 1 24
Osa04LNT0271600.2 osa-miR5809 Cleavage 4.5 14.582 1 20
Osa04LNT0271600.2 osa-miR5820 Translation 3.5 23.112 1 21
Osa04LNT0271600.2 osa-miR5079b Cleavage 5.0 19.705 1 22
Osa04LNT0271600.2 osa-miR5079b Translation 4.5 20.6 1 22
Osa04LNT0271600.2 osa-miR5539b Translation 4.5 14.406 1 22
Osa04LNT0271600.2 osa-miR160c-3p Cleavage 5.0 23.968 1 21
Osa04LNT0271600.2 osa-miR160f-5p Translation 4.5 23.251 1 21
Osa04LNT0271600.2 osa-miR413 Cleavage 5.0 14.497 1 21
Osa04LNT0271600.2 osa-miR535-5p Translation 5.0 23.928 1 21
Osa04LNT0271600.2 osa-miR1875 Translation 4.5 19.415 1 24
Osa04LNT0271600.2 osa-miR1877 Cleavage 5.0 17.127 1 24
Osa04LNT0271600.2 osa-miR2093-5p Cleavage 5.0 23.805 1 20
Osa04LNT0271600.2 osa-miR2101-3p Cleavage 5.0 12.865 1 22
Osa04LNT0271600.2 osa-miR2874 Cleavage 5.0 11.272 1 24
Osa04LNT0271600.2 osa-miR2876-5p Translation 5.0 19.878 1 21
Osa04LNT0271600.2 osa-miR2876-5p Translation 4.5 19.294 1 21
Osa04LNT0271600.2 osa-miR2920 Cleavage 3.5 18.0 1 23
Osa04LNT0271600.2 osa-miR5079a Translation 4.5 20.6 1 22
Osa04LNT0271600.2 osa-miR5144-5p Translation 4.5 16.899 1 21
Osa04LNT0271600.2 osa-miR5157a-3p Cleavage 4.5 13.278 1 24
Osa04LNT0271600.2 osa-miR5157b-3p Cleavage 4.5 13.278 1 24
Osa04LNT0271600.2 osa-miR5505 Cleavage 4.0 20.332 1 22
Osa04LNT0271600.2 osa-miR6255 Cleavage 4.5 15.06 1 22
Osa04LNT0271600.2 osa-miR417 Cleavage 3.5 11.393 1 21
Osa04LNT0271600.2 osa-miR5079a Cleavage 5.0 19.705 1 22
Osa04LNT0271600.2 osa-miR5338 Translation 3.5 14.059 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0271600.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0271600.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0271600.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0271600.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0271600.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0271600.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271600.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271600.2 4 nan Morphological trait Culm/leaf RM3785 RM1388
Osa04LNT0271600.2 4 gpp4 Morphological trait Seed RZ569 RZ565
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