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

>Osa12LNT0128700.2

CGTGTCCGAAAACCCCTTCCGATATTCGGTCAAACGTCCGATGTGACAATCAAAAATTTTCTTTTCGCGAACTAAACAGGCCCTAAACAACCTACAAATGCCAACAAGGCCTCCAGCTTCTGCATAAAGCAACGACAATCGGGAATCAAATCCTTATGAACCTATCGCCAGAGGTTGATACATCGATCATGTATATCGACATGTGCCTTGAGTTCTTGAATTTGGAGGGCGATTTGATGGCGGGCAGGCACATAGTTGCTTTGATCTTCCGGACCGCCTTCCAGACCAGTCTATCCTTGTCCTCTCTAGGATGAAGTTGGTGCAGGAAGATGTCGATACAGTCCTCAATATCGTAGGCCAGTTCCCGCACCTTGTCCTTCCACTCCTAAGTCGATAAGCTTCTGGAGAAGGGAATTAGGCAGCTCAGCTCATGCTTCAGGATTGCAATCTCTTTTTGAACCCCCTTGAGTAGCTTGTATTCATCGCCGAGAGCGTCTTTCAGCGCTATTTTCTGAGTCCTTGTACTTCAATTATAGATATTAAACGTGGCACGTATGTCTTGAAACCTTGGATGCCTTTGGACGGCGTCCCTGTATGCAGGCACCTTGCTGGAGTGGCTTGTCACTTGGACCTCTTCAAGCCTTGGTAGGTGCTCGATGCCAATAAGTGGAGTTTTGCCATGTTGCGCCGCTCCACTGGTGCCATGCCCTTCCTCCAAGTTAGAAGGCTTCTTGTCATCTAGCTTCAGAATCTGAAGCTGTGGCATTGCCCCTGGCTCAAACGTCAGGCATGCCAAATCACATGTTAAAACAAATTTCTGCAGCTTTGGGAAATTGTCGGTATGGGTGATTCTTCCCAAACGCGTGGTAACGCGTTTAGTGATGATGTTCTCAGGGGTAGCTTGAGCAGTCAAGTCGAGGTCAACAAGGCAGGGCAGCCCAGCAAGAAATTGGACGTCGCGGCAACTGAGCTCCTCAACACGAAGCTCTAGCATTGTGAGCTTCAGAGAAAACCACAGCCAGGATGGGACATTGCGAATGTTCTTACGGATGATGAGTTGCTGAAGCCATAACGATGCAAAATTCAGAATATGCGGTGAACAAGCAACCAAATTTGGCGAGAAGAGGTCCGAATGTGAGGAAGCTGGTGTATCCAGATGCTGAGATAGGTAGTCCAGAATGGATTCAGTTGGCCAACCATCATCGAAACTTGGAAACTCAAGGGAGGCAGGGGGAGAACGAAGACCTCCATTGGTAGAACGAAGACCTCCATTGTTGAAACGACGTGTTTTTGCCAGTCTGATAGCAGATGAATTAAATCGAGAAATTTTCTCCACAATAGTAAAAATGTCGGGCAAACCCCCTGAATTAAAGGTCAACAAAGTTTGTAGAGAGACCAGTTTCTGAATCCCATTAGGCAGCACTGCATCACCTGAAACTGTTAGATGACACAATGATGATAGAGAAATAACATCTGATGGAAAACCAGTAACCAAAAGGCTGCCTAGTAGATCTAGTGTCCTCAAACACTGGAGTCTCCCAATTTTCTGAGGCAGCTTTAACCTGAAACCTCTGATACTCAAGTGTCTCAACAGGAAGAGGTTGCTCACAGCAGACAAATCAAGGAAAACGGATGTAGAATAGGCCCTAAGTTCCAATACCCGCAAATGCTCAAACATAGAAATAGGAGGCTGCATACTGCAGCCAAACGCAGGGAAAGTATTATAGGATCGAACCTGTGATAGTTTCATTCTTTCCATGGCCAAGTTTCCGTATGACAACTGATGGCACAGACGACGAACTGGAAGCTTTGTTACATTCTTTACAGGCTGCTTAGATGCTATAGTGATGAAGTTTTCCTCCTGGCACTTCGATATTATAAGGTCAAGCATAAGGTCATGGACATGACATGCCTCACTGGAACGATAATCATCTAGCTTAATCATACTCCTATTAATGAGTTCGTTGAAATAGCTCTCAGCTGTTTCCTCCAGATCCAAACCAGGTTTCTCATGGATAAATCCTTCAGCTATCCATAGCCTTATCAAATCAGCTTTGAAAATTGTATGGTCTTCAGGATATATTCCTAGATACAGGAAGCATGTCTTGAGATTATGTGAGAGGTCAAGGTAGCTCAGATTCAGTACATGTCTCATCCATTCTAGAGTGGGATTTGTTTCCGACTCAGAACCCATAAAGTTATGAATCTTCTTCCACTTACCCACATTCATGCCTTCACTGGATAAAAGGCTAGCAATGCTAATGATTGCCAATGGGACACCTTTGCATTTTCTTAACATATCTTCTGATACATTTTTATACTGCTCAGGAATACTATCCGAATCAAATATCCTTTTACAAAATAACTTTTGTGAGTTAAACTCATTAAGTGGCTCCATCTTGTACACCATACCATGGAAATCAACGCAACACTTTGTAGCTACATCTTCGATTCTTGTTGTAACTATAACTCTGCTACCATGATTATTTTGAGCAAAAGCACACCGAATAATGCTCCATGCTTGAGTGTTCCATATGTCATCAACTACAATAAGGTACCTCTTATTAGCAAGATGTCCTCTGAGGGTGTCAATGAGCTTTTGATGGTCATCAAGAATTCCGTAGCCTTGAAATCCTGTTCCTGAAAGTAAATTTCTCAGCAGCTTAACCATGTCAGGGTTTTGAGACACTGACACGAATGATGTGAAATTGAATCGTTTTTTCAATTGGTTGTATACTTGTTTGGCAAGAGTTGTCTTGCCAATGCCTCCAAAGCCAACTACAGAGAGAACTTTAAGTTGTTGTATCGAACCATTCTCTACTTCATCCATTAGCCACTGAGTAATTTCCATACATGGACCGTCAATGCCCACAAGATTTTTTGCATCTTCATAGAGTGCAGGTAGACGCGGATCAACTTCCACCACTTTGGGAATGCTTGAGGTAGATACACCTAGATTGGCATACCTATCACGGCGCTCAGCCACCTGCATGACACGAGCCTTGAGTTCTTGAATCTTGTCGGCAATCTGATAGCGAGCACGCAAATTCCTGAGCTTGCGTGCAGTCTTCCTGAGCAAGCCATCCTTGTTATTACCATCACCAAGATGGTACATGAAGACATCAATGCAGTCCTCGATGTCGTAGACCATCTCGCGGATGTCATTCCTCCACAGCTTCTGCTGTCCATCTAGCTTCTCCATATCTGCAAGATTCTCCAACACAGCATTCATTTCGGTCAACTCATGGCTAAGGAACTCAATGTTCTTACGCATTCCCTTGAGTTTCTTGCACTTGTTGCTGAGCAGCATGGCAAGTTTGGTGAGGAGTGGCGCCATGACCCCCATGGAAGAGTTCACTGCTGCCATCATAAAACCAATGTGTTTGCTCGCCTTTGCTCAATGGGCTAGCTGGTCAGAGTGGATGCCAAATCATGAGCCGTCACTGTGTCCTCCCGTCACCTGGCATACGTGCTGATGACGACCCAACTTGGTGCTTTGCATCCTCTTGATGGACATCAGAATCAGACAAGAGTCACGAAATTTCTTGGAATCTCGTCTACAATTTCCCAGAATTGGTTTGTTTTGTCTTCAGAATATGTCAGTATTGGTAGTGGTACAGTACTACAGTTCACTATCTATTGACTTGTTGGCCGCGTGATGCAGATCAGCAGACGGACGGACGGACTACAGGCCCGTCACCCGCACACCATTCATCCGAAGCCCGGCCACGACGCCGGCGTTGGGGCCGATCCATCCCCGACCACCGTCCGCCTTCGGCCCGGAGACCGACGTACGGATCGGAGGCACCGGTGCGGAGCTCGATCCCACGACAGATTGAGGCGACGGCGGAGCGCTTACCAGCAGAAGGGAGCGGAAGTGGATAACCTGGAGGATGGATGGCGTCCTGTCCCGTCTAGAGCTTGGCGGCCACGACGCGGAGGAGGAGATCGGGGAAGAGGAGCACGTGCTCCGCCGCGCCGCCGGCGAACCGCCCGCCGGCGAGCGCTCGAGGAGACGAGGTGGGGAACTGGGGATCGAGGAGTCGGGTTTCTGCGGATCAGT

Coding Potentia
Explanation CPC Score
noncoding -1.17382
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0128700.2 12 16590649 C A
Osa12LNT0128700.2 12 16592171 A C
Osa12LNT0128700.2 12 16589426 G A
Osa12LNT0128700.2 12 16589603 A G
Osa12LNT0128700.2 12 16589786 A C
Osa12LNT0128700.2 12 16589806 G T
Osa12LNT0128700.2 12 16589907 C T
Osa12LNT0128700.2 12 16590212 A G
Osa12LNT0128700.2 12 16590388 T G
Osa12LNT0128700.2 12 16590484 A T
Osa12LNT0128700.2 12 16590601 A C
Osa12LNT0128700.2 12 16590729 A G
Osa12LNT0128700.2 12 16590925 C G
Osa12LNT0128700.2 12 16591003 T G
Osa12LNT0128700.2 12 16591356 C T
Osa12LNT0128700.2 12 16591375 A G
Osa12LNT0128700.2 12 16591605 T A
Osa12LNT0128700.2 12 16591654 T C
Osa12LNT0128700.2 12 16591666 T A
Osa12LNT0128700.2 12 16591810 C A
Osa12LNT0128700.2 12 16591905 A T
Osa12LNT0128700.2 12 16591955 A G
Osa12LNT0128700.2 12 16592099 C A
Osa12LNT0128700.2 12 16592403 T C
Osa12LNT0128700.2 12 16593020 T G
Osa12LNT0128700.2 12 16593552 C G
Osa12LNT0128700.2 12 16593584 G A
Osa12LNT0128700.2 12 16593590 T G
Osa12LNT0128700.2 12 16594081 C T
Osa12LNT0128700.2 12 16594146 T G
Osa12LNT0128700.2 12 16594183 A G
Osa12LNT0128700.2 12 16594253 A G
Osa12LNT0128700.2 12 16594258 A G
Osa12LNT0128700.2 12 16594278 A G
Osa12LNT0128700.2 12 16594630 T C
Osa12LNT0128700.2 12 16594774 C A
Osa12LNT0128700.2 12 16594832 G C
Osa12LNT0128700.2 12 16594939 G A
Osa12LNT0128700.2 12 16594953 T C
Osa12LNT0128700.2 12 16595256 T A
Osa12LNT0128700.2 12 16595326 C A
Osa12LNT0128700.2 12 16595422 T C
Osa12LNT0128700.2 12 16595509 C T
Osa12LNT0128700.2 12 16595726 C T
Osa12LNT0128700.2 12 16592210 T A
Osa12LNT0128700.2 12 16595817 A G
Osa12LNT0128700.2 12 16591503 T C
Osa12LNT0128700.2 12 16595001 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0128700.2 osa-miR5542 Translation 5.0 8.628 1 21
Osa12LNT0128700.2 osa-miR5822 Translation 4.0 22.531 1 21
Osa12LNT0128700.2 osa-miR5822 Translation 4.0 21.13 1 21
Osa12LNT0128700.2 osa-miR1437b-3p Cleavage 5.0 24.792 1 24
Osa12LNT0128700.2 osa-miR7692-3p Cleavage 4.0 17.778 1 24
Osa12LNT0128700.2 osa-miR7692-3p Translation 5.0 19.807 1 24
Osa12LNT0128700.2 osa-miR1861o Cleavage 5.0 21.076 1 22
Osa12LNT0128700.2 osa-miR395a Translation 4.5 18.679 1 21
Osa12LNT0128700.2 osa-miR397b Translation 5.0 12.583 1 21
Osa12LNT0128700.2 osa-miR408-5p Cleavage 5.0 8.889 1 21
Osa12LNT0128700.2 osa-miR1426 Cleavage 5.0 19.791 1 21
Osa12LNT0128700.2 osa-miR1426 Cleavage 5.0 19.989 1 21
Osa12LNT0128700.2 osa-miR1441 Cleavage 3.0 12.497 1 21
Osa12LNT0128700.2 osa-miR1861a Cleavage 5.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861b Cleavage 3.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861c Translation 4.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861d Cleavage 4.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861e Translation 5.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861f Cleavage 3.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861g Translation 4.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861h Cleavage 4.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861i Cleavage 3.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861j Cleavage 4.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861k Translation 5.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861l Cleavage 3.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1861m Translation 5.0 21.076 1 22
Osa12LNT0128700.2 osa-miR1861n Translation 3.5 21.076 1 22
Osa12LNT0128700.2 osa-miR1870-3p Translation 3.5 11.82 1 24
Osa12LNT0128700.2 osa-miR2873b Translation 5.0 20.225 1 21
Osa12LNT0128700.2 osa-miR5156 Translation 5.0 18.644 1 24
Osa12LNT0128700.2 osa-miR396f-5p Cleavage 3.5 13.395 1 22
Osa12LNT0128700.2 osa-miR396e-5p Cleavage 4.5 14.272 1 21
Osa12LNT0128700.2 osa-miR2918 Cleavage 4.5 16.324 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM511
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM28166
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM511
Osa12LNT0128700.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM28048 RM28166
Osa12LNT0128700.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0128700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0128700.2 12 nan Morphological trait Seed RG543 RG81
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