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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa01LNT0055500.1

CTGACACCAGCCAATAAAATATCTTCACTGTATCGGGGTAAAGTTACAACACCGAATGGCGGCTTATAAGAGGTATATACATGAAGGTGAAACCCTAAAGGATAACGATCCATACCGCGGGGGCGCTTCGCTCCAGCAGAAACTGATATTTATTATGTGCAAATGAACTTTGGTTCACAACTCAACACCGATCGATCATCATCCAGTTCCCCGCCGCCGCCTCCGCGTGTCATGGGCGCAGGTGAATCCTCCAACGGGCTCACGCTCGGCATGCACGGTATCGATCCTCGGTGGCGTCGCCTTCCTTGGCGTCGCAGGACGGTGCAGTGTAGGGCGCGCGCGGCCACGTCGAGTCATGACATGAGCACGCCGACGCCTGGAGGGAGGCGGCCGGACTTCTTCTTGGTTGACGGAGATGCCCCGGAGGTAGATGCTGTTCGTCGAGGGGTTCATTGGTCCTGACCTTGGTCGTTGTAGGAGAGGATGCTGCTCACGTCGGACGGCGTCGGCGGACAGCGGCATCAGATTGTACGGCCCACTCCCGAAGAAGGACACGCCACGCCGGACGTGGCGCCTGTGACGGCGAACTGCCGCTTGAGCGACAGCTTCGAGTACCACGGCCGAGGCCAGAGGACGCCCCTGACGGAGCTTCCAGCCTCTTGAAGGTGAAATAATATTCAGAAGTTGTTGGAATTGACTGATTTAGAATTTTGCTTCGTCCCTCCTTTTTTGCTCTCTACACATTCTGTCCTGGGCAAAAGACCGCTTGATCTATGGTTCACTCTGCCTTGATTCGCTCTCTCATCCATCGATTGCTTGTCCCGGTATAAATATTTCACCATCTAACATAATCTTTGGGATGCGAGATATCTTGTTAGCATCCTCCCTTTGGCACCATTCAGCCAGTCTTGGACAAAAATAAATATATAATAATTCTAAGGTGGTAATGTTCCATATGCTCTCTGGCAAAGATGTCAAGTTGGGGGAATCGAAGATGCTAATTTCTTTCAGATAAATGAACTGCCCTATCCATTCCGGAAGGCTATTGAACCCTTCCAACCATAGTTCTTCAAGAGCAGTAAGATTCTTCATGCTTTCAGGCAAATATGTCAAATTGGGAGAACTTTGGATATCAAGGCATTTTAGGGCAGTGAGATGTCCAAGCAATTCTGGCAGGAAAGTCAGCATGGGGCAATCGTTAATGACAAACCTTTTCAGTGGAATGTGCAGCCCCAACCCTTCTGGCAGTATCTCTAATCCTTTGCATCCATCCAAACGCAACTCTGTTATAGCGGTTAGGTTCTTCATACTACTAGGCAGAAAAGTCAACTTAGGGCAATCGATGATGATAAACTCCTCTAGGGAAACGAGCATCCCTAACCATTCTGGCAATATCTCCAGCCCTTTGCATCCATCCAACAGCAGCCTTATCAGAGCGGTTAGGTTCTTCATGCTTTCAGGCAGAAAAGTCAATTTTGGGCAATCCATGATGATAAACTTCTCTAGGCAAATGAGCAGTCCCAGCCCTTCTGGCAATATCTCTAGTCCTTTGCATCCATCCAACCACAGCTCTATAAGAGCGGTTAGGTTCTTCATACTTTCAGGCAGAAAAGTCAACTTGGGGCAATTGTTGATGATAAACTTCTCAAGGGAAATAAGCAGCCCCAACCCTTCTGGCAGTATCTCTAGCCCTTTGCATCCATCCAACCGCAGTTCTATAAGAGCGGTTAGGTTCTTCATGCTTTCAGGTAGAAAAGTCAGCTTGGGGCAATCGATGAGGACAAACTTTTCCAGAGAAATGAGCATCCCCAGCCCTTCTGGCAGTATCTCTAGCTCTTTGCATCCATACAAATACAACACTTTCATAGCAGTTAGGTTCTTCATACTTTCAGGCAGAAAAGTTAGCATAGGGTAATTGTTGATGACAATTTTTTTCAGAGAAATGAGCAGCCCTAACCATTTTGGTAGTGTCTCCAGCCGTTTACAGCCATCCAACCGCAGCTCTATCAGAGTGGCTAGTTTCTTCATGCTTTCAGGTAGATAAGTCAGCTTGGGACAATTGCTGATGACAAACTTTTTCAGAGAAATGAGTAGCCCCAGCCCTTCTGGTAGTGTCTCTAGCCCTTTGCATCCATCCAAATGCAGCTCTATCAATGCGGTTAGGTTCTTCATGCTTTCAGGCAGAAAAGTCAGCTTGGGGCAATCCATGATGATAAACTTCTCCAAGGAAATAAGCCGGCCCATCCCTTCAGGAAGTGTCTCCAGCCCTTTGCATCCCCGCAACAACAGTTCCCTCAGAGAGGTAAGGTTTTGTAAGCTTGTAGGCAGAGTAGTCAACACAGGGCAATTGATGAATTCAATGACTTCTAGGCAAATGAGCTGCCCCAGCCATTCGGGCAATATTTCCAAGTTCTCCCACGAGCACAAATATAGCTCTCTGAGGGAGACGAAGCTTTGAAGGATGTCTGGAAAGGTCCTCAGCCCACTGCAACCTTCAACTTGAAAAATCTCAATGGTGGCAAGATGTTGAAATCTTACCCACATGTCAGGGGGATATTTGCAGTTGTTGATGACCACACGAAAAGGAAGAGTGGAAGATGCAAGGCTCCCAAACCCTCGTTCTGGCAACACCTTATCGCTATTGTCCAATGACCAGTGCATACTTCTAGGGGGATACGGGAGGAAACTCAACTTTGGGCAGTCAACTGCCTTCAAAAAATGCAAATTAGGGATTAAGAACTCTCTATCTTCTTCACCCGACCGCGTTGTCCACCATTCTTCGAAGTTATCCATTCGTTCTAACCAAATAATTCTTAATTTCTTGCAATTCCCTTCCCCATCGTAGAATTCTCTGCCAATTTTTCTAATGGTGGGCATATTCTTCATACAAAAAAATCTCAGGTTTGGCAACCGTCCAAATGCAGGAAGAGAATCACATGTTGCTAAATTAGAAAGACATAAGTAAATGAGACAAGGGAGGTAGGAGGAGATGCCAGACACCCAGTTAGGGAAATCCTTGCACATGTACCATAAAACTTTCAAGAGTTCGAGGAGGTAATAGGTTCTCAAGCACCTCTTCATCCTTGTCCACATTTCTCGTGCCACCAAGTCCCCATGACAAAGTTAGTTCCCGAAGGTCAGTCATATCACGCAACTTAGCTTCCCTTGCATTGTCCAGCCGCTCAACATTTTCAAGATGTTGAATTCCCAGTGCACGACAACTTAGTTTCCCAAGCTCCACTATACTGCAACACTCTCCATTTTCTATCTCATGTACATCATGTTCTTCACGGCCAGGTAAATTTAGACACTCTTTAATGGACCAAGCCTTATCAAGCACACCTTTTGTTCCTGAAATAACATCAAGCAGCGTGAGGCTAGCCATGTCGCTGATACTATCTGGCATGTCTCGCAGACTATAACAACAAGTAAGGTTCAAGACTTGAAGTTGAAGGTCACCAAACAAAGACGGAAGATGTTCAATCCTTATACAATATGACAAATTGAGATGCTTCAACTTAAATATGTTGCATAATGATTGGGGTAATGACTGTAGCTTAGAACAGCTTGTGAGGTTCAAAAACTGGAGCTCAGAAAGGTCCCCGAAGCATTCAGGGAGTTGTTTGAGGCCATGGCAGTCTGAAAGATTGAGGTCTTTCAAATGTTTAAGTTGGCAGAAGGATTCTGGTAACACTGGAATCTTGTAGCAATCAGACAGGTCCAAAACCTCTAGTCTATAAAGAATCCCAAAATCTTCTGGTAGGTTTTCTAGCTCATGGCAATCTGAAAGGATTAGATGCTCAAGAGACTCAAGGTTAAAATTGCCTGGTAGTTTGGTTAGCTTTGAACAACTTGTCAAGTTTACAAATGAGAGCTTAGAAAGGCTGCCAAATTCATCAGGGAGATTTTGAAGAGCACAACAACCTGACATGTCTAGTTGTTCTAAGCATTTAAGGTTGTGGATTGATTCAGGCAATTCTTCAAGTTTAGTACACCCAGATAGGCTGAGGAGAGAAAGTTTGAGAAGGTTTCCAAATGATGTCGGAAGTTTACTGAGGTCACTATTCCCTGATAAGTCTAGATAACAAAGCTTGTGTAGGTTACCAATATTAGCAGGCAAGGTTTCAAGAGAGCAATTGGATAGAATTAGAGTTTGCATATTCTGAAACATATGCAAATATTTAGGAAGTGCTGCAATTGGCAAGCCTGAGACATCAAGATAAGCTAGCAGCATCAGTTGACGAATGGAGGATGGCAACGCCATACTAACAGGGATAGATTGCCCTTCAGACGAACATCCGCTCAGGTCCAAGATCCGTATATACTTTGACCCAGAGAATGCCTTTCGGGGAAGTTGCGATCCAATGCACTCCCTAAAATGAATGGTTCTAACCTTGCTTGGTAGATCTTTGAAAAACTTGGGTTGCTTCTGGTAGTTGACCAACTGTGCATGTCGGCAATAACGCTTATTATTAGCTTTGCTCCATGTATTTGGCATGGTAGCGTCCATGACAAGGAATTCATCAGGAGCAATTATTGTTGCGAGATCATGCACTAAATCATGCATGGTGAGCTTGCGTGGAGCTTTGGTGTGCATTGGACTAACCATGGAAGACTTGGAAATCTGAAGAAAGGACATCCGCAAAAGATAGTTGACACACCTTTGACCATTATCTCGTGCTTCAATGTATCCAAGGGCTATCCATTGCTGGATCAAGCGATCAGTGTCCATGACGAAACCCTTCGAAAAGGCTGCCAAATATGTAAAGCACATTTTGAATTCTCGCTTCATATAGTAATAGCTCAACATTAGGCGCTCTATAGTGTCTTGCTGATGATCTGCTTTGAAATCCAAAACAATCTTTCTATCCCTTATATCTGTCCATGCCTCAACCGTCCTATGTTCAGACATTACTTGCCCGAGAGCATTTGCCACCAGTGGTAGTCCTCCACACTTCTCGGCAATTTGCCTTCCAATTTCCTCTAAGCCATTTTGGCCATCATCAGGCCCAAATACTCTCCGCTTCATGACGCTCCAGCAGTCGTAAGGTGATAAAACACCCAAATTGATATGATCAGGCTCAGGCACCGGACATACTTTCCGTTCATTTGCAAGATAACCAGTGTATAGTACTTGCACTACGCTTCCACTACGTGTAGTTGCTATAATCTTGCTACCCTTTCCGCCATGTTGTAACATCTGCTTCAACTTTTCCAAATTTTCTCCATATTCTTCCCAGAGATCATCTAGAACAATCAAGTATCTTCTGTTGGCAAGTTCTTTTTTCAGATTATTGTTTACAAACTGCAAGTTGCAGTTGTCCAGGTTGATACTTCTGTTTGCTCCTCTGATGATAGCCTTCCCAATTTTGAGCAGGTCAAACTCCTTGGAAACATAGACCCAGATTCGCAAATCAAAGACATTGACCCTTTTGTCTGCAAAAACTGCTTGGGCTAAGGTAGTCTTCCCTAGTCCACCAAGCCCAACAATTGGGATGATTGAGATATCCTCCTTAGCTTCAGTGTTCAACAGAAGGTTGATTATTTTTTTTGTTTCGGCATCCCTCCCTAGCATTCCAATGTCCACGTCACCATCATCTGCAAAAGTTTCATTGTCTCTACTCCCTTCTGCCACTAGTTCACGATGCACATGATGAAGCTTAATGCTATCCTTTTTTATTGAGACTATTTTCTCCCTCGAGTTCTTCATGTTGCGGGCTATGGTCATCTTCCGGAGAAGCGGATTGTTCCGGGAAAGGAATAACTTGAGCTTGGGTTGATGGTTCTTGATGAGCTGAGCAGCATCGAGCTCATCCAGCACGTCCTCAACGTCGTAGGCGACGGACTTGAGTTTGTTGAGCCACCGCCGTTCCGCCTCTCCATCTTTTCCTCCCTGGCGTGCTTTGCCATCAACATCTTGTATCACAGCCTCCAGATCTCTCATCTTCTCCTCCATGTCGTCCACGTCGTCCTTGAATCTCCACAGCAGAGTGGCCTCCTCCACCACAAGCTCGCTGAGCCTGCTGGCGACCCGATTCGCCACGGAACTCGCAATCATCCCTCCAATCCCGCTCATGGATGGTATGGCAGATTCACAGTGAACTCACATGGCACAGTTCACGTAGTTTAGTCCATGGCATAGTGCGCTTGGTAGGTGGTGCGTGGTGGCTTGCCTTAGATGCGCAAGCTACCAGACAGCTAGCACATGCGCAAGCTCTCTCTCTCTCTCTCCCACAGGAATGTATGCTGCCTGTTTGTTTGTGAAAGCTCTCTACCCACAAGTGCACTTCGTCTCTTTGTTTTGTGGAGGACCCTACCACAGTCCACAACTGCATGTCCATGAGAGTTTTTCCTTGCGATTGGCATGCTCCACCAATATGTCGCTTGCTTTACCCGTTTGCCCGCCAAATAGATTTTTAGTGGCACAATTTGCATCTCTTTGTTTCTTGACCTGTAGCCTTTTTGCATCGACACGATTTGCAAGCATCATCCCTTTGAAGAAAGAAGTATTGTTGAGACCATGGCTTGGCACGCTTGGTGGATGGTGGGTGGCGGCCTTCCTGGCACAACACCAGGAGAGGCGCCGCCGCTGCACTTCCGCCTGTACCGAGCCGACCCGAGCCGCGGGACACAGGGGCGCATGGTGCTCGACTCGATCCATCGATCCGGCCGCCGCCGCTCGAACGGACGCCGCCTCCAGCCCCCTTCACCACCTCGCCGCCGGTGGCTTCGCTCCGCCCCCCGTGGCTGGACTCACGGGATCGTCTGCG

Coding Potentia
Explanation CPC Score
noncoding -1.00533
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0055500.1 1 41156654 G T
Osa01LNT0055500.1 1 41160209 C T
Osa01LNT0055500.1 1 41155861 A G
Osa01LNT0055500.1 1 41155876 T C
Osa01LNT0055500.1 1 41155885 A G
Osa01LNT0055500.1 1 41156002 G C
Osa01LNT0055500.1 1 41156137 A G
Osa01LNT0055500.1 1 41157155 C T
Osa01LNT0055500.1 1 41157313 C T
Osa01LNT0055500.1 1 41158313 C T
Osa01LNT0055500.1 1 41158571 C T
Osa01LNT0055500.1 1 41158580 A G
Osa01LNT0055500.1 1 41158795 G T
Osa01LNT0055500.1 1 41159613 T C
Osa01LNT0055500.1 1 41159950 A G
Osa01LNT0055500.1 1 41160243 G C
Osa01LNT0055500.1 1 41160939 A G
Osa01LNT0055500.1 1 41161032 G C
Osa01LNT0055500.1 1 41161149 T G
Osa01LNT0055500.1 1 41161856 T C
Osa01LNT0055500.1 1 41161884 A C
Osa01LNT0055500.1 1 41162376 T C
Osa01LNT0055500.1 1 41163247 G A
Osa01LNT0055500.1 1 41164521 C T
Osa01LNT0055500.1 1 41165027 C G
Osa01LNT0055500.1 1 41158011 T C
Osa01LNT0055500.1 1 41163415 G A
Osa01LNT0055500.1 1 41162266 A 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
Osa01LNT0055500.1 osa-miR5536 Cleavage 4.0 17.727 1 22
Osa01LNT0055500.1 osa-miR5791 Cleavage 5.0 12.817 1 21
Osa01LNT0055500.1 osa-miR5791 Translation 5.0 18.495 1 21
Osa01LNT0055500.1 osa-miR5829 Translation 5.0 9.761 1 24
Osa01LNT0055500.1 osa-miR6249a Cleavage 4.0 19.311 1 21
Osa01LNT0055500.1 osa-miR6249b Cleavage 4.0 19.311 1 21
Osa01LNT0055500.1 osa-miR319a-5p Translation 4.5 17.148 1 21
Osa01LNT0055500.1 osa-miR319a-3p Translation 5.0 10.331 1 21
Osa01LNT0055500.1 osa-miR426 Cleavage 4.5 19.238 1 21
Osa01LNT0055500.1 osa-miR815a Translation 4.0 8.223 1 21
Osa01LNT0055500.1 osa-miR815b Translation 4.0 8.223 1 21
Osa01LNT0055500.1 osa-miR815c Translation 4.0 8.223 1 21
Osa01LNT0055500.1 osa-miR816 Cleavage 5.0 22.393 1 20
Osa01LNT0055500.1 osa-miR816 Cleavage 5.0 17.21 1 20
Osa01LNT0055500.1 osa-miR444b.2 Cleavage 4.0 13.747 1 21
Osa01LNT0055500.1 osa-miR444b.1 Translation 3.5 18.359 1 21
Osa01LNT0055500.1 osa-miR444b.1 Cleavage 4.5 16.341 1 21
Osa01LNT0055500.1 osa-miR444b.1 Cleavage 5.0 20.347 1 21
Osa01LNT0055500.1 osa-miR444b.1 Cleavage 5.0 21.298 1 21
Osa01LNT0055500.1 osa-miR444c.2 Cleavage 4.0 13.747 1 21
Osa01LNT0055500.1 osa-miR444c.1 Translation 3.5 18.359 1 21
Osa01LNT0055500.1 osa-miR444c.1 Cleavage 4.5 16.341 1 21
Osa01LNT0055500.1 osa-miR444c.1 Cleavage 5.0 20.347 1 21
Osa01LNT0055500.1 osa-miR444c.1 Cleavage 5.0 21.298 1 21
Osa01LNT0055500.1 osa-miR444f Cleavage 3.5 13.747 1 21
Osa01LNT0055500.1 osa-miR1861c Cleavage 4.5 18.719 1 22
Osa01LNT0055500.1 osa-miR2102-5p Cleavage 4.0 23.567 1 20
Osa01LNT0055500.1 osa-miR2863a Cleavage 5.0 12.472 1 21
Osa01LNT0055500.1 osa-miR2863a Translation 5.0 16.456 1 21
Osa01LNT0055500.1 osa-miR2870 Translation 5.0 23.998 1 21
Osa01LNT0055500.1 osa-miR2863b Cleavage 4.0 13.077 1 21
Osa01LNT0055500.1 osa-miR1862f Cleavage 5.0 16.951 1 20
Osa01LNT0055500.1 osa-miR1862g Cleavage 5.0 16.951 1 20
Osa01LNT0055500.1 osa-miR5145 Cleavage 4.0 13.939 1 24
Osa01LNT0055500.1 osa-miR5146 Cleavage 5.0 16.032 1 24
Osa01LNT0055500.1 osa-miR5486 Cleavage 4.5 14.715 1 21
Osa01LNT0055500.1 osa-miR5499 Cleavage 4.5 22.73 1 21
Osa01LNT0055500.1 osa-miR5814 Translation 5.0 13.773 1 24
Osa01LNT0055500.1 osa-miR1862e Cleavage 5.0 17.082 1 24
Osa01LNT0055500.1 osa-miR1854-5p Translation 4.0 7.002 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0055500.1 1 qNOP-1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0055500.1 1 qPHT-1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0055500.1 1 qPL-1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Drought tolerance C86 RZ14
Osa01LNT0055500.1 1 yd1b Morphological trait Seed C547 C2340
Osa01LNT0055500.1 1 qPH1-1 Morphological trait Shoot/Seedling C86 RG236
Osa01LNT0055500.1 1 pl1.1 Morphological trait Panicle/flower RZ730 RZ801
Osa01LNT0055500.1 1 qPHT1-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0055500.1 1 sd-1 Morphological trait Dwarf RZ730 RG810
Osa01LNT0055500.1 1 qRIE 1 Resistance or Tolerance Submergency tolerance C86 G54
Osa01LNT0055500.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0055500.1 1 nan Morphological trait Root RG109 RM104
Osa01LNT0055500.1 1 FSM Morphological trait Shoot/Seedling nan nan
Osa01LNT0055500.1 1 rrw1b Resistance or Tolerance Other soil stress tolerance C86 RG236
Osa01LNT0055500.1 1 grl1-1 Morphological trait Seed RM431 RM104
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 qRNd1 Resistance or Tolerance Other soil stress tolerance RG236 C86
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other soil stress tolerance RZ730 RZ801
Osa01LNT0055500.1 1 tn1-4 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0055500.1 1 nan Morphological trait Seed RZ730 RZ801
Osa01LNT0055500.1 1 fll1 Morphological trait Culm/leaf RZ730 RZ801
Osa01LNT0055500.1 1 ph1 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0055500.1 1 nan Morphological trait Root RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Other disease resistance RG109 RG236
Osa01LNT0055500.1 1 sd1 Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Drought tolerance RZ730 RZ801
Osa01LNT0055500.1 1 Fh1-2 Morphological trait Dwarf RZ730 RZ801
Osa01LNT0055500.1 1 nan Resistance or Tolerance Drought tolerance RZ730 RG810
Osa01LNT0055500.1 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0055500.1 1 nan Resistance or Tolerance Drought tolerance RG810 RZ730
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