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

>Osa01LNT0029300.1

ACCTAAGATGACTTCATGGTTATTACCAAATGCATGTACAACATGCAAAAAACTTTACAAGTGGTTTGACAAACTGAAATTTGCAATTAAATAAAATAGCCAGTTGAGCAAAACATATTAATCCCTGACCTAATCTGAATCCGAAGCTCCTTTCACATGGAGCAAATTACTGATCAAATGTGCTCCGTTACAAATCAGTACTCACAGTTCCTGGCTCCTGCTTACGTCCTCACACAAAACTTAACACTCACTGAAGACAAGTAAGGACTTCATCTTGAATTTGTTCATAACAGTGAATTGCTTCATCCTGGACCTGGCTGCTTCTCTCCTGATCACCTGCAACTCCTCGGCGAGCAGCCGACTACAACGGTTTTGGTCTCTGAGTCAGCCATAACGAGGAGGCGGCCGGAGGGACTGCTCGGGGAAGGAGTGGATGTAGGCATATACAGGAGAAGGGGCAGACCAAGAAAGTAAATGTTTACTGCTTTTCTAATCTGTGAGGACCTCTCTATACACAATATTTTTTGTGTATGTTGCAGCTTGTTTAGACAATTCCTTTCCTTTCTTCTCATTGTCCTTCACGCCAGTACGCTTAGACTTTTTCTTTTGTTTCTTGTCTTCTACCGGCATCGATAGTATTTTTATGTTTGTTCTAGAGGTTGCTCTTGACAGTGCAACGTATAGTTGACCATGGGAGAAGACAGGCTCTGGTAAGTAGACGCCTGCATTTGGAATTGTTTGACCCTGCGCCTTATTGATGGTCAATGCAAAGCTCAATCTAACCGGAAATTGCTTCCTCTTGAAGCGAAATGGGAACATCTCATCATCAGAAGGACATAGAGGTATCCGAGGAAGGAAAACTCTCTTTCCAGCATGCTGCCCTACAACAATCTCCGCGTCAATAGCATTTTTTCCGAACTGACGAACCACCAGCCTTGTCCCATTGCAAAGTCCGTTGGCTGTTGGCTGGGTCAATGTTCCTCAAAAGCATGATGGGGCAGTTTATCTTCAGCTTAAGCAGATGCGGAGGTAGCCCATTTGGAGTTAGAGAGTTCAAGAATTTTGGCGGGTAATAGTTATGAGGGTCATCCTCTGCTCAGTCAAAACTATGATATGTCATCACATCTCCTCTAAACCGCTCAATCATCTTCATGTTTATTCGATCGACGAACTCATTCCGAGTGGACAATATGGCCCTACATATGATGTAGTTTGGGTCCGTCAGGTTATCGTTTAGGTTAGGGAACACGGTATCGATGAGCCTTTCGAGGTCCGTTTCATTCCCTTTGCACTCTAAGCAAATATCCGAAGGAAGGCCTATGTTTCCTTCCTTGTTCACCTCCTCGGTTCCATTCCCAACTCGAAGGAGGTAGTCCGCAAACCACGCGTCGCTCTGCGCCCTCATATTGCGAACAAGCTTTAATTGAACCATACAATCCCAAAGATAGGACCTGCGTAGAGTGGCTTCTGTTATCTGAGACCTAGTGCCCTTCCTAATGACCGGGAGCACCTGCCTGAAATCCCCTCCAAACACAATCGTCTTCCCTCCAAACGGAGAACGTGGACAACCCATTATATCTCTCATGCTCATATCGAGGGCCTCAACCGCTTGCCTCTTTGTCATGGAGGCCTCATCCCATATTATAAGCGATGCCATCTGGAGAAGCTTTGCCGTCCCACTTTGTTTGGTGAAGCTGCAATACGACCCTTCCTCAATGTTGAGTGGGATCTTGAACCGCGAATGTGCGGTCCGGCCTGCTGGCATTATAGAAGCTGCAACACCCGACGTCGCGGTTGCCACCTCTATATCACCATTGCCACGCACTGTAGCTAGTAGCGCCCTATATAGGAAAGTCTTCCCCGTGCCTCCTGGGCCATCTACGAAGAACACGCTCCCCTGAGCACTACCAACCGCGTTCATGATTTTATTGAATGCAGACCTTTGCTCATCATTGAGCTGGTCTGGGAGGTTCATATCATCTCTCTCCACAACAATGGAAGACTCCTCAATAATCTCTCTGGGATCTCCTCGAGTACTATCATGTGATTCATCTATTTCAGGGAGCGGGAACGATGAGATTTCCTTACCCATTGATTGTAGCATGCCCCGGATATCTATCAGCACCATCTGTTGGACAGCATAAGGGCATGCGTTGTTACATCTGACATGGAATCTAGATGCTTGTCCCAAAGTGCACGGACATCGGTAGGTTCGCAGTACACCAATATGGTAGCGAATAACCTGCGTAGCGACGCCGGCATTTGGTAGACACCGGCCTCCGTAAGGCACTCGTCGAGGGTGTTGTCTGCCTCTATAAGACCCCTTCTTTCAGCTGCAGCACGGAACGACGGCATGAGCACACCATCAACAGTACGTAGGTCTTCAAATGAGGTGGATCCTGTCACATGGTTTAGAAGCACCCGAAGATAGTAGCGCTCCCCCTCTGCCGGGTGGGCACACACAATTCTCCCGACCTGGCCACCTCTATCTCTTTTCTTCCAGTACTTACCTGGCGTCTGCCAAGTAAACCACATTGGGAAATCTCTATAAAGGATATCTCGAGCCTAGACATGCTGCCTGTTAGCCTCGAAATACGCCGTAAGCATCGATCTGCCTGCGTCTTCCTTATCCAGAACATCACGGAGATCCTTGTCTGCATCGAAAGCCAACATGTGCATGTTTGGCAGATGCAATTGCAACTGCCTCACAGACGGCGAGATGTGGCATATGTCAAAACCATATATACGCCACAAGGCTTCTGGAGGGGTCACCCACCTCGCATCCCTGTAGCGCTGAATCTCATCGATTTCACCGTTTTTATCTGCCTCGTTTATGGATATCGAGGCCTTGTCATGTCCCTTGTAAAGGTATTTAAAGAGGTACTTTACTGCCTTGATGCTCGAGCAAATCTCGACATTCATGTGACAGTTGTACATCCGTAGAAGATAAGGATTGTACGGGACAACCCACCTGTTATCGAGAGGATGTCCTCTAACCACCTTACTCTTACTGTCATTACGTCTCCTATACAACGGGTATGAATCCTTGCCTTGCGAGGTTGTGGTGTTGAACTCTCGTAGGTAGTTGTTCCTGCACTTTCCATCTCGCATGCATTGGCACCTACCGTTGAGTCGACCACAAGGGCCATGCATCATATGCTTGACAACCATATTGTATAGCTCTGGATATTTTTTCTTGTCCGGTAGCTCAGCTGAGACGATGCGGTCATATTGCTCTGCAGACGTTAGCTTGTATCGACCACTCATGATCAGCAAAAAGTGTGCGTGTGGCAGACCCCTCTTCTGGAACTCAACAACATATACGTGTGCAATGACTTTGCCAAGGATGTGCTTCTCGAACAGCTGCTTCTTTAGGTCCTCTAACTTGGCTCGAAAGACACGGACCACGAGATCAAGACGATCTTGTGGTGTCTGGCCAGGCTCAAGTTCACGAGTAATCTCATCCTACTTGGGGTTGCTAGTCATTGTAAGGAATACATCTGGCTTCCCGTACTTCTATACTAAAGCCATGGCATCCATGTATCGACGCTTCATATTTCGGCCACCACAGACAAACAAAGCTGGCAACACAGTTCTTTTGCCAACCGCGCTTGCTCGACTCTCCCCAGCCTGGATGCTATCCATCAACCCTTGATACAGGTCCGCCCTTATCTCCTTCTGGTTGTTCCTCACATAGTCTAGACGGGAGCTCTCAACCTTGATGTACATGTCAACGGCAAACTGCTGGAACAGGAGTCCGCCGTGAAGTATAGGATTGAAAATCCCACGACGCATCTGGAATTTATAGCAGTAGTAGTCCCTTACAGAGACTCGTATCCTGCTGTTACAATCTACACGTGAGAAACATCTAGGTTAGTACAGTCATGTAACGCACAATGATCAATTCTCTAAGGCAACATAGTACGAAGATAAACTTACCAGGATCATCGCCATTCCGTGCGTTTGCATCCTCCATGGTTATTTTGTCCTTTGGAAGGCTTTGATGCCAACCATTCTCTCTAGGGAAGAAAAGAGGGTACGAGAGGGGATCATAACATTCGTAGAAAGGCTGGATAGATTTCCGCGTACGGTTGTTCCTGTATATTGTCACGCTAGGCTCGAACTTCCTTCTCTCATTTCCCTCAACCCAGATAGCAGCGACCTCAGTTGTCACCGGCACATTGTAACGCCTTTGGTGCAACCTATGATCCAGATTTAGTGTCACGCGATAATTCGCGAGGTCTTCAGCCTGCCCTAGACTTCTAAATGTCTCCGAGTACGGGTTGTTCCGAAGGACGTCTGCAACAGTCCTAATCACATCCTGGTCAAGGCTAGGGGAACGTTGGAATCTATGACTCAATGTTGGATCGTCATCGTAGAAATACAACTCGAGATGCTCTGGACCAGAATCTCTAGGACTGAAAGAATGTATATTATGATATATCTGACCATGAGCCCGAAAAGTGTACACGCCCGAACTCATGTTTGCAAAGGCCTTGTCAAGGCTTACACCAAGGGTAGTGAATGAGAAGTGGCCGTTGAAGTATCTATTGTTATCACGGAAATGCTTGGCGTCTGGATCCGAGCTTGTCCAAAGCCTCATCAGTTCAGGAGGTGTTTCATTTTGTACAAGCTTGATCTTGCCACCCCGACAACAGAAGCTCGGCGGTTCGTACTGGAACCTCTTGGCACCACAGTGTTTACAGTCAGGTTCAGGCTTCAGAACATTTGTGCTTTGTGGAATGTTGCTGTACATATAGTCATACGGATCAGGAACAGAAGAGGTCGGTGATTGCGTGTCATCGTCATCAGATTGTACCATCTCGTCATCCTCATCGTCGCCTAGCCCAGCAAACATGTAGTATTCATCGTCGGAGTCATCATCCATGAAGGAATCCATATCATCATCATTGAATGTGCATGATCGCGCCTGATGATCTACAGCATGCTCAGTTTGCAGGCTCGATGTAGATGGCACATCACCGGTTGTTTCCAAGCAAGGCGTTGGATTTAGCAACAATGGGATAGATCCCTCAGGGCACTCTAGTGCAATGGATTCAGCGCATGGTTTGTCACGCCTAGCTGCATAGAGTGCGTTACGTCGTGCCAGATGAGCAGATCTTTCCCCAGGAGTAACATTTTGTCGTCTTGATCTACGGCAAGCATTCATATCATGGATTTCCACATCTGGCATAGATTGCCTTGCAACCCTACGACGGGCATTCAACTCTAGTCTCTGTTCTTTTGTTAGTGATTGACGTTGTGTTCTCCGTTGGTCCACCTTAGCTTGCTTTTGCTCCGGTGTAAGAGTTGCATACTTCTCCCTAGCTCGAGCTAGCTTTGACTGCAATCGTTCTTTTGTCTCATTGGTTGGCGCACGCACCAATTCATTATCTAGAGAGATGTCGTCATCGTGGTCGCACTCATTTTGATCGCTGCCTTCAAAAAAACTGGATTCATATTGATTTTCACATCCTGAATTATCAACTACAAAGTCAGAAGTATTCATGTTTAGGTACTTTGAGTGAAGCGACTCATTGGTACTTCGTTGGGACCATAGTGAGCTACATTGTTGATGATTGTAAATGGGAGACGTCTTGGTGTGATATTAAGATGGGAAGCTTCACTTTTTCCTTGATGCAGCGGGGAAGAATCAGTCACTTCCAATTGGCACTTCATTATATCAACAGCGCTTATATTTGAAATATCGCCAAGTGGGGCTGAAACTTGAGTTTCCTCCTTCTTTCTTTTCCTTCTTTCACGTGCCTTCTTGTTCCTATCATCTTTTTGCTCTGGGGTCAATGCTGCGTACCGGTCTCTAGCACGCTTTCTTTTTAGTTCAGCCACACTAAGGTGACTAACATCTTCATGCAAACCTGTACACATATGCACATTGCTGGGTGTATTGAAGGACGCATCGCGGTTTTCCGCACATGGATGACTATTAGGCGTCACCACAGGATGCACAACATTTGAAGCAGTTGGGAGTGTTATTTGTAAAGACATCACAATTCTCGTCGTATCTTTCAACGGCACGTAACGACTTGTTTCCAACCTTGCCCCGTCAATTTGCCAAACCGGAACCACTTATATTGGTTATGTCAGCAAGAGGGCCTGATTTTGTAGTTGATGTTGTGGAGCCCCCAACAATCTTATCCATTTCTAGAAAGGATATATATAGAGAGGTGCAGCACTAAAAACACCAGGATGGCTGTAGCCTGGCTAGCGGCGTGGGGGCGAGGAGGCGCGAAGGGGACCAGACGACGAGTAATCGACGACGACTTGTTGGAAACCCAATGTAAGAAATTCAATCAAATGCTGAAACACTGATCTGATGTTGAGGAGGCCGGAAGCTGGCAGCAATATTCTGAAGTTAAATTCAACTGTTATTAGATACAAATCATGAGTTTAGGGATCCCAACAGCGTTGTCCATTGCTGTAGGCCAAGGCGTGGAGATCAATAACCACCGTGTAAGGCGTCGGCGGCGTCCTGGCGACGGGTACCCTGACAAAACATGCCGTTGCCAGCTGTCGAACTCCAAATTAGGTGCTTACAATTTACAAGATCAAAACTGATTGCTCTATCGGAACTATGGACAGCACAAAATAATCCGTCAGTGGTTGTTAAAATGCATTTTACTGGGTTAAAGAAGCCGATGCTGGATGAGCAGGGTGTGATTCACTATATCATTGGGGATTTTGACACTGGATTCTAAAGTTTTTCCATGAACAGAGTGGCAGATTGTTTCTGCGGCATTCAATCGAACACCTCATGTGCATGGGCAAAATAGCTTTACTCGTTCATCGCAATCAAAATCAATTGGGTAGTATAAGTCAAAATAGTTTGCTCATCACAATCAAAATCAAATCGGAAGGGAGAAGAGATTGAAAGACAACAAAAGAGAAAACTTGCCGTACAGCTCTACTGGCCTCAAACCACCTCTCCGCTCGGTCTCGGCATTGTAGCGGCGTGAATCCCTTTCCTCAGGCGCTCGGGAAGATGATGTCGATGACCGCGGCGGAGGTGGCGGCTGAGGGGATAAGCGTCGAAGCAGAGGAGGCGGGGCGGCGGGCGATATAGCGCGGAGGCGACCACGAGAAGATGGATGAAACAGCGATGGGGGAGGTGGCGCGGGTGTGGGAGATCGGCTTGGGGTGGGGGGGGGGGGGCGACGACGACTCAGGCGACTCCGGATCGGTGGCGGCGAAGCCGTCGGCACACGCGGAGGCGGTCGACAAGTCGGAGATTGGGGGCGGCGCGGAGGACACCGGCGAGGTGGGAGACGGCGCGGGCGGCGATTAGGGTGCGGGCGTGCGGCGTTGGAGGTTGTTGAGGGGG

Coding Potentia
Explanation CPC Score
noncoding -1.30446
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0029300.1 1 26062491 A G
Osa01LNT0029300.1 1 26063811 A G
Osa01LNT0029300.1 1 26064996 C T
Osa01LNT0029300.1 1 26065801 A T
Osa01LNT0029300.1 1 26067852 C T
Osa01LNT0029300.1 1 26066293 A T
Osa01LNT0029300.1 1 26069832 T C
Osa01LNT0029300.1 1 26071212 A T
Osa01LNT0029300.1 1 26068245 G A
Osa01LNT0029300.1 1 26070814 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0029300.1 DTM_#DNAt_MULE_japo_Os0202 Chr1 - 26066570 26066789 219
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0029300.1 osa-miR5794 Translation 5.0 15.446 1 21
Osa01LNT0029300.1 osa-miR812v Cleavage 5.0 11.312 1 24
Osa01LNT0029300.1 osa-miR5813 Cleavage 5.0 20.749 1 22
Osa01LNT0029300.1 osa-miR5822 Cleavage 5.0 15.283 1 21
Osa01LNT0029300.1 osa-miR5822 Cleavage 4.5 22.0 1 21
Osa01LNT0029300.1 osa-miR5834 Translation 4.5 22.717 1 21
Osa01LNT0029300.1 osa-miR396a-3p Cleavage 5.0 20.497 1 20
Osa01LNT0029300.1 osa-miR396b-3p Cleavage 5.0 20.497 1 20
Osa01LNT0029300.1 osa-miR398b Translation 5.0 21.72 1 21
Osa01LNT0029300.1 osa-miR164e Translation 5.0 6.044 1 21
Osa01LNT0029300.1 osa-miR167e-3p Cleavage 4.5 18.193 1 21
Osa01LNT0029300.1 osa-miR167h-3p Translation 5.0 18.193 1 21
Osa01LNT0029300.1 osa-miR167i-3p Cleavage 4.5 18.193 1 21
Osa01LNT0029300.1 osa-miR169i-5p.2 Cleavage 5.0 14.157 1 22
Osa01LNT0029300.1 osa-miR444a-5p Cleavage 4.0 16.936 1 21
Osa01LNT0029300.1 osa-miR818a Cleavage 3.5 20.022 1 22
Osa01LNT0029300.1 osa-miR818b Cleavage 3.5 20.022 1 22
Osa01LNT0029300.1 osa-miR818c Cleavage 3.5 20.022 1 22
Osa01LNT0029300.1 osa-miR818d Cleavage 3.5 20.022 1 22
Osa01LNT0029300.1 osa-miR818e Cleavage 3.5 20.022 1 22
Osa01LNT0029300.1 osa-miR1442 Cleavage 4.5 22.546 1 20
Osa01LNT0029300.1 osa-miR2092-5p Cleavage 4.5 12.815 1 21
Osa01LNT0029300.1 osa-miR2095-3p Cleavage 4.0 17.498 1 20
Osa01LNT0029300.1 osa-miR2097-5p Translation 4.0 21.446 1 22
Osa01LNT0029300.1 osa-miR2097-5p Translation 5.0 9.401 1 22
Osa01LNT0029300.1 osa-miR2875 Cleavage 3.0 19.71 1 24
Osa01LNT0029300.1 osa-miR2879 Cleavage 5.0 14.711 1 24
Osa01LNT0029300.1 osa-miR5159 Cleavage 4.5 23.13 1 24
Osa01LNT0029300.1 osa-miR5484 Translation 4.0 22.21 1 21
Osa01LNT0029300.1 osa-miR5491 Translation 5.0 18.825 1 21
Osa01LNT0029300.1 osa-miR5505 Cleavage 5.0 21.615 1 22
Osa01LNT0029300.1 osa-miR5513 Translation 3.5 18.728 1 21
Osa01LNT0029300.1 osa-miR5524 Cleavage 4.5 7.57 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0029300.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0029300.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0029300.1 1 nan Morphological trait Root RM23 RM306
Osa01LNT0029300.1 1 yld1.1 Physiological trait Source activity RM5 RG462
Osa01LNT0029300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0029300.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0029300.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0029300.1 1 nan Morphological trait Seed CDO118 CDO455
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