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

>Osa02LNT0169900.1

TGAATCTGAAGCCAAATTATTTTTTTGTTCATCCTAGCCTAACTACTACTACTAATAAACAAAGAAAAAGGGAAGCTCAATAGTGAGATTTAACTTTCATCTCCCTAGATAAGCTGTTATATTTGTTTATGTATATACATAGTAATAAAACTGTAAGATGTCTCTATTTAATAAATGACTAAACTGTGGTATAAAAAAACTTCTATTTACACAGATAAAACCAGGTTCCCATCCTTTCGGTGCATACTACTACCTGTCTACCTGGCTAGCACCTCTGTCCCTGTTACAACAACCGTCGGTCATACTGAACCTTTGCATGAGCCAGTTTTCCTCATGGAGGTAACAGGCAAAAAAAAACATGTGCCTTCCTCCAGAGAATCTGCATCTGTCATTGACGGCAAAGGCTACCAACGGAAGCAACCAGGTGGAGAAATGCCAAAGGAAGTTCCTAGCTCTTCCCACCAAGGCGCTCATAGAACAAGATATAGCCATGATCTGTGTTGCCACCACAATGCTCCCGAGAAGAGCCATAGAATGTTTGCAGGGTGGATTCCTCGCTGATCTGGACGGTGTCATCGTCGAAAGAAAGCCAGTTACCATGGCTTTTAATTTGGCTTACGTAGTGTCCATGGTTGGGGCTGCTCCCAACATGGACTACAACCGCAAAGAGGGAGTACTCGCAGTCAGCGTCTTCAGACATGCTGCCCAGCTTCAGCTCCAGGGGATATACCACTCGGTACGACAGTTTCTTGTGCCGGCTAAGCTGCTCAACGTACTTGAAGCGCTTCAGGTGGATCACCAATACGTGTGGCGCCTTCTTTATCTTCATTCTCTTGTGTGCTTCTTGCAAACTGCTGCATTTGTCACAAAAGAACTTATCCTCGCCATTTAAAATCTCAGTGGAAAAGAAGCTCTTCAGGCAGCTTGTGAGCGAACTATTCTGTTCCACGTCAATGCTCAAATCAAAAAACGTCTCATCTTTTGCTGTGATAGTATCACACATTAGGCATTTGGTTTCATTGGTCAAAATACCCTGAAAAGTCCTGTGCACCAATGTAACTAATGGCCTTTCTCTGGCTCCATTTGCTAAAGCATTGGCTGCCCCATTTGAGACCTCTTCAGGAGTAGTCTCAGGAGAACTATTTGCAGTTCTACAATCTTCTTCAAGAATATCAATAATATCATTCACTAAGAAATTCCAGAACTCATGGGCATCCTGGTGCATATAACTTCTGAACAATTCATTCTGTTTCCTCACTCTTTGAACAAAACGTTTTGGTGCAAGAACACCAGTCCTTTTCTTCGCTAGAGTTATCTGCAAAAAATATCATCAATCTGTTGGAAGTGCCTGCTACATTTGCAAACTAATCAGGAAGAGCGGTGATCGTTAATGCAAGATCCTATAACAGGTTTATGGCATGCTTTAGTTGCAACTTCCAACTTTGTTCAATGCGGCTTCAGGGTAAGTTATCCAATCAGTCAGATGTATAGAAAGCAGAACAAAGTTGTCAGCAAGCACCTTGCAAAGCTGAGAACTGAGGCAAAGCAAACAACAATGATAATTGGACTGTACAAAAGAGTTTGCATAAGCAAGTGCTTAGGAAAGCTTAATCTCTCTTCTGAAGTAAAAGAAAAAAAATATTGAATCGACTGCTATATACCACAGTAATTATCCTCTTGATTCAAATAAGAAAGAGACTGTCAATAACTATGGATAGAAGAACTCTCGTTTACCAAAATTTAAGTGGTATTTGGACAATGATACGGTTCCAAAATATTATTCTAATCCAATTTCCAATATCATTTGTTGTTATTAAATAAAAAAGTAAATGCATTATAAATGCATATTTCATAATGAATCCTGTTTTATAACCAATTTATGTTAGAAAATTTAGAATATTTTTCACATATTGATTATCAAAATTAAAAATATCTTACTACGCACATTCTAGGAGTCACTTATATGTAGCAACAATGGAATTGGTACATATATTCTTTTATATGAAGAAATAATACAACCAATAAAGTAGTATGTCAGCTAATAACGAGGTTTTTTATGCTCCTCCTTCACCTGTGAAAAAAGATCAGCCAGACAAGTCAACAAATTGTCCTCGGAGTCTTCTGTGTTTTTGTAAGTTGCATAATATTCCAGCAACTGCTCCCGAAAAGGGATGCAATGATAAAGTGCCTGAAGAAGAAGTACAGTTTTTTAGATTCACAACAGTGTAACAAATATTTCCTATGAAGTTATTCTTAGCAAGCATGACCAACTGATCTGTGTTAAGAACATGATCTACATTATTACTAATGACCAATCAGGAATAAGAAACAAAACCTAACTTTTAAAATGAAGTGAAAGATACTTAATTGCATTGCATTCCTTCTTATCACCATCTGACCCACTGCTCATATACTAGTGAGAACTAAGAAGTGAGAAAGCTTAAAGCTAAACATGGTCCAAGTGTAGCAGTATAGATAGCATCTTAAATAAGAATCCTAATCTTCCATAACAAACAACTAAAGGTTAGTGCACCCTCAAAAGGACATAAAATTGTTGATATTAAGCTAACACTGATTATAAAAACATTTTTGTGGTATAAAAAGTTTCTATTTTTAAAAAATATATTCATCTGATTTGTAACTATATAGTGTTACTTAACTAAATTTCCTATGAAGCAGATAGAATACTCAGTCACTCAGATGACACCACTGTTTCATATTCCAGGATACTTTATTCAAAAGTTACTATTAGAGAACCAGACCAAATATACAAAATCGATGACATATTCACAACTGAAAGAGGATCCTAAAGAGTTGTTGAGGAAAACTGAAGAACTTCACAAGAATCATGAAATCTGAACACCTATCTTGAAATCCGCCTGTGGCTTGTGATACAAACCTGTAAGCATTGTACTAGGAACAGGTTTTTTACTTTGTTTACATTGTACTAAGAAATATTTTTTACATGCAAACATCTGTGCCACTGTATTCAGTTCATGCCCTTAATAGTCAATACCACACCATCAATGGCTTTAGAATTCAGAATAGTACTTTCCATGTCATTTGGTATTAGTATAGGCAACCCACACAATAGGTCGTTTATATAATTGATTGTAAGTTGCAACAGCTTCACATGATTAATGAGTTGGCTGATTGCCACGGAGCATGTAGCCGAGTGGACTAAAGCATTTAACCACCTTCTCCTATTAAACATCAGCCAAATGAACAGAGGAACCCAGTTACTGCTGAACCATATGTATCATCTTTGCCCATGACTCTCCATCCCATGAACCCAAACAAACAAACAATAAATAAATAAATTCACTGGCTAGTCCCTTGAACAGTGCCGGGCCTAGAACAATTTGACGACTAGGGCAACAAACCAAAACCACCACCACCACCACCACCACCGATCTCGGAAGAAACTACACACACAAACATTTTCTCATAGAACTCAGATCATACGGACACTTAACCAACCCGGAATTGCCGCGCATCACATCCATCGAGCAGCGGAGAAGGGGGGCCGGCTGGGGTTAGGCAGCTACCTGCAGGACGCTGTTGCAGTAGCAGGTGTTGCCGAAGTTCTCGAGGCCGAAGTAGCGCGCGCCCTCGGGGAAGTGGTCGCCGAGGGCCTTCTCGAGCTTGGAGACGCCCGCGCCGAGGACCGAGAGGCGGTCCCACAGCCCGGACGCGGCGCTGGAGAGCGACCGGAGCCCCGACCCCGCCGCCGCCGGCCGGGGCCTCTCCGCGGCCGCCGCCGGCGGCGGCGGCGGGTCCTCCGCCGCGAGCAGCCGCGCCGTCCTCGCCATCCCCTACGGATGGATGGATCGCTCGGTTCGAACGCGCGTGGCGGCGGGCGGATTAAGGGGGAAGAAGAAGGCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.596043
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0169900.1 2 21986817 G A
Osa02LNT0169900.1 2 21988109 T G
Osa02LNT0169900.1 2 21989391 T G
Osa02LNT0169900.1 2 21989580 T C
Osa02LNT0169900.1 2 21990217 A G
Osa02LNT0169900.1 2 21991141 T 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
Osa02LNT0169900.1 osa-miR5837.1 Cleavage 4.5 19.072 1 21
Osa02LNT0169900.1 osa-miR319a-3p Cleavage 5.0 15.563 1 21
Osa02LNT0169900.1 osa-miR2104 Cleavage 4.5 11.638 1 22
Osa02LNT0169900.1 osa-miR2275a Translation 5.0 14.367 1 22
Osa02LNT0169900.1 osa-miR2275b Translation 5.0 14.367 1 22
Osa02LNT0169900.1 osa-miR2864.2 Translation 4.0 19.937 1 21
Osa02LNT0169900.1 osa-miR5144-5p Translation 4.0 13.31 1 21
Osa02LNT0169900.1 osa-miR5156 Translation 5.0 16.547 1 24
Osa02LNT0169900.1 osa-miR5487 Cleavage 5.0 11.946 1 21
Osa02LNT0169900.1 osa-miR5490 Cleavage 3.5 13.025 1 21
Osa02LNT0169900.1 osa-miR5509 Translation 4.0 20.576 1 21
Osa02LNT0169900.1 osa-miR5509 Cleavage 4.5 23.997 1 21
Osa02LNT0169900.1 osa-miR5515 Cleavage 3.5 13.372 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0169900.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0169900.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0169900.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0169900.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0169900.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0169900.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0169900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
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