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

>Osa02LNT0172000.1

GCATGAATTTTCTTTTTTTTTCCCTGTAAACAAGAAAAGCAGAAGCTTTTTCCTATTTGCCCATATGCCCAGCAAACAACTATCGCTTCCTCCACTACATCAAAATTCGAATTTACAGCAGGAAGCAATTGGACAAACCGAAAACTAGAGAACGAACGAACGAAAAATCTATAAGCCGCTGGGCAACACCTTTTGCCGCTGGGAGCTTTAGCACCTGGATCACTAATTCACTATGTGCAAAGAACCATTTGGTCCTCTCATTGCTTACCCACCTTGCGGCCTGGCCATGGCACTTCAAAGATGGCTACATACATACACCCGACAACAGCTCGGAGTACCGCAAGTCGCGGCCATTATGGCTGTGCCGTCCTCCAAGCACATATGATGATTTGTAGGGCAGGTTACCGCGATACTCCAGGCGCATAATTTACGACATCCAGCAGCATCAAAATTGAGGGCCTTGTTCGAGCTAGTTTGGAAGCAGAAGGAAGGAGCGTCTACCATATGCACAGCTAATTCAGCAACTAGCCCACAAGCACTGGGACTAGTTGATCTCTCCTTCCTCTGCATCTTTAGTGCTGGGGACACTGCTAGGATCTTCTTCCTCTTCCTCCTCATCTGCTTTCATGAAGAGTCCCAGCTGTTCCAATGGATTGCCTGATCCAGGAAGAAAACTGGGCATGCCATCCTGGGAATGCTCAGGACTAGTCTCATCAACAGAACTCACAATATGTTCTGTGGTTGCCGTTCCAAGCATTTCCAAATCCTTTAGATGGAGGTTGTCATTGATTTCCACCGTTCTCTCCATCTGCATTAAGTTAAACCACTCAAATTTTAGCGGGAAAAAGAAAGCTCGACACCAGTAAATGCAGTTTTTTTCACTAGCCTCCTGCAGGGCCTGGCGAGCTTTCTCCCTCTCAAGGTCCCGTTTACGCTTGGCTTCAGCTTCAGCTTCAGCTCTTCGAGCTTCCATAGCTGCATTTCCTTCAGCCAACAGCCTTGCTTTCTCTTCCTTCTGGAGCTTTTCCAGCTCCTCCTGTTTGTCTCCACCCTGGCTGAGAATCCCCTGTGCCTTAACAATCACATCAGCATAACGACTCCTAAGGAGGGCTGCTCTTAAGAGCTTGTCTGGGGAGACTTGCCTGTCGGGTTTTGAATTCTCCCCCTCTGGGGCAGGCTTTGACTCGTTATCCTGCTCACGGAGCTCCACATCATCAGCAGGACGGATGGCATCGACTGGACTTATAACATCACTCTTTTCTTGCTCCACCAGTTGTTCAGATCTCTTACTTCCCTTCGGCTTTCCTGGGCTACCACCTTTTTCTTGTTCGCTTTCACTGTCACTGCCCGACTCAGAATCGCTGGAAGAAGATCCAGAGTCACTGCTGGAACTACTTGGGCTACCACACTTGTTAGGATTGTTGTGTGCATCTTTTTCTATCAATATAGGGGATGCATTCCCGCAAATATCTACATCCTCCTCAACTGGATCACCACCTTTGCAGGGATTTGTAGAGGAGTGGCTAAGGCCAGATACATTAGCAGCCTCATTCTCAGAAGGCTCAGATTTTGCCTGCTGGCTCTGCTCTCTCTCTTGCAAATACTTGTCAACATGTTTCTTCAACTCGAATAGTAGGTCATCACTGACAGCATGGATATCAATCTCTATCTCTCCATCACCAAGCTGATCTGTGTTGTTGTCAATGCATTGCTGCAACAAATCAATGATGTGTGAAGGTACCTCCGGATCCTCAGACAAAGATGCCAAACAGTTCCCAAATGATTCTTTCTCCTCGAATGTCATTTTTGGCTTTACAGACTCTGTTGGTCTAACAGACTCTGTTGGCCTCACACACTCTGTTGACACCTCACTGCAGTCCACAGGGGGAGTCTTCCTCCTCTTTGAGTCAGCCCTGTCAACCTCGACGTGCGCCTCTGTGGCAATGGAAGCCAGCTTCTTTTCAATTGTCCTCCATCTTGATTCAAACATCTTGTTTAGTTGAATGGCATAATCATGCACTACATGCCCACGAGGATTGTAAGTCATCGCATTTGAAAAGGTCAGCCGTACATCGGCTGCAAATTCAGATGGACTCGTGTAGGAACCAGAGTCAAGCTTATTCCTGATAGTTCCAAGATCCATCGGTTTCTTGATGATTTGAAAATAATCTGGAATATTCAGCTTAACAGCATCAACCGGGGAGTCGAATATGTTACTACATTTCTGAGTCATCAGCTTTTTCAGAATAGCATCGCATTGCTTAAAAATCGCATCCTCAGTCAACACCGTGGAAGCCTCAGGTCGGGGCTTTGTAGGCAAGAAACGCCCCTTGGCACCACGGACCACATGGTTACCACGCTGTCCCTTCTTACCTCGAGGGGCAGCCGAGGACGAGAGCGCGGGAGCTCTATTGACAGGGACAGGGACAGCAAACTCCGGCTTCTTGAGGAGATTCCGGACCGAATCAAGCTCTGTGCGGAACCTCTTCCGGAGATGCCTCCTCTCGGAGGAGGACATCTTGGCTGGGACGAAAATCTCCCGCTTGACATCGAAGCCGTCGCTGTTTAGGCTGATGCACTTGCGCTTGGGGGCCGAAGAGTCCTCGGAGTCAACACGAACGGGGCTGCCTGCCGCGCCCTCCGACTCGCCAACGGTCTCCGCGTAACCCCGTGGCGCCGCTGACGCCATGCCCCGGAACGCCATTTCATCGTAGCCCCGCTTAATCTGCCTCTGCTGCCCAAACTCCATGAGGACCGTCGGTGTCATGTGCCCGGGCGCCAGATCTGAAGAAGCCGGATCTGAAGAGGGCGAAACCCTAGGCCGGGGATCCGCGGCGGACGGCGGCCTCCTCCTCCCGTGCGGCCGCCGGCGAGCCGGATCTGCTCCGGAGACGGGCGGATCTGAGGGTCGCGAGGTGGCCGCCGGCTCGAGACGCCTCCCCGCCTTATCCTCTTTTTTTTTTCTCTTTTTTCTTCTCTTTTCTTTTTCCTCCTCTCGAGTCGAGCCGTCTCCTGCTTATCCTTTTCCTTCGCGAAGCGACTCGACTTGAGCCGAGCCGAGGTGGAGGGAGCCGAGCCGAGCCGGGGAGAGCCGAAGTGGAGATCCGCGCGGGGGAAGCGAGAGACCCGAAACTGGGAAGCGAAGCGATGCGAGACTGTGACGCGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.85507
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0172000.1 2 23551476 A G
Osa02LNT0172000.1 2 23549621 A G
Osa02LNT0172000.1 2 23549641 A G
Osa02LNT0172000.1 2 23550114 A G
Osa02LNT0172000.1 2 23550904 C A
Osa02LNT0172000.1 2 23551558 C T
Osa02LNT0172000.1 2 23551784 A G
Osa02LNT0172000.1 2 23551790 A G
Osa02LNT0172000.1 2 23551913 G A
Osa02LNT0172000.1 2 23552606 C T
Osa02LNT0172000.1 2 23552798 A G
Osa02LNT0172000.1 2 23552936 T C
Osa02LNT0172000.1 2 23553629 A C
Osa02LNT0172000.1 2 23554262 C T
Osa02LNT0172000.1 2 23554321 A G
Osa02LNT0172000.1 2 23551812 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
Osa02LNT0172000.1 osa-miR5527 Cleavage 4.0 17.716 1 21
Osa02LNT0172000.1 osa-miR5790 Cleavage 3.5 18.409 1 24
Osa02LNT0172000.1 osa-miR5791 Translation 4.5 24.774 1 21
Osa02LNT0172000.1 osa-miR5821 Cleavage 4.5 11.191 1 21
Osa02LNT0172000.1 osa-miR168a-5p Cleavage 4.5 9.364 1 21
Osa02LNT0172000.1 osa-miR169b Cleavage 5.0 15.93 1 21
Osa02LNT0172000.1 osa-miR169c Cleavage 5.0 15.93 1 21
Osa02LNT0172000.1 osa-miR169e Cleavage 5.0 15.93 1 21
Osa02LNT0172000.1 osa-miR169n Cleavage 4.5 15.93 1 21
Osa02LNT0172000.1 osa-miR169o Cleavage 4.5 15.93 1 21
Osa02LNT0172000.1 osa-miR171d-5p Translation 4.5 20.684 1 21
Osa02LNT0172000.1 osa-miR171e-5p Cleavage 5.0 24.168 1 21
Osa02LNT0172000.1 osa-miR171e-5p Translation 4.5 20.684 1 21
Osa02LNT0172000.1 osa-miR171f-5p Translation 5.0 20.684 1 21
Osa02LNT0172000.1 osa-miR437 Translation 4.5 18.711 1 21
Osa02LNT0172000.1 osa-miR444a-5p Translation 5.0 24.301 1 21
Osa02LNT0172000.1 osa-miR816 Cleavage 5.0 17.502 1 20
Osa02LNT0172000.1 osa-miR818a Cleavage 4.5 17.356 1 22
Osa02LNT0172000.1 osa-miR818b Cleavage 4.5 17.356 1 22
Osa02LNT0172000.1 osa-miR818c Cleavage 4.5 17.356 1 22
Osa02LNT0172000.1 osa-miR818d Cleavage 4.5 17.356 1 22
Osa02LNT0172000.1 osa-miR818e Cleavage 4.5 17.356 1 22
Osa02LNT0172000.1 osa-miR529b Cleavage 4.0 20.388 1 21
Osa02LNT0172000.1 osa-miR529b Cleavage 5.0 3.181 1 21
Osa02LNT0172000.1 osa-miR5153 Translation 5.0 18.76 1 24
Osa02LNT0172000.1 osa-miR5499 Cleavage 4.5 8.185 1 21
Osa02LNT0172000.1 osa-miR5499 Translation 4.5 17.309 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0172000.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0172000.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172000.1 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0172000.1 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0172000.1 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0172000.1 2 nan Others Others C424 G45
Osa02LNT0172000.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172000.1 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0172000.1 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0172000.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0172000.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0172000.1 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0172000.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0172000.1 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0172000.1 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0172000.1 2 yld2.1 Morphological trait Seed RM262 RM263
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