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

>Osa07LNT0390700.2

ATAATAATTAAGAGTTATAGGATTCCAACCATAAGTGCTTGGTCATAGTCTGGATTGCAGTTTCATGTAAAGCAAAAGGATTCTACGAAGCAAACGCCATATATATGACAGCAGCTATTTACATTAGTGGCCATAATGCAGAGGTTCTAAACAAATGGCGTTGCTTCTAAGGGTGGGTGTGCATACTGGTGACATCCTGGACATATAACCAAAAGGGACAGTAATGTGCTGCATGTTGTTTCCTTCTTCATCCGCTTTTCTTATGTTTCTGCTGACTGTCATCTTTAAATAGTTTCTTAGCAGCTGAGGCTGAGGCTGAGGCTGCAGGCCTTTTTGGGGGAATGTTTTTGGTAGGCGGTGATGGGGATGCTGATGGAGTATCTTCTGCTGCTATTGCTAGTGCCTTTGCCTTGTCCTGAGTAGCAGAAGATAGCTCAACAGACGATGCAATCTGCGGAGGTTCTCCCTTAATTTTTGTCTCAGTTGTTGCCTTAGGATCATGTGAGAATGAGATCTGTTTATCTTGAGCTGGCTTGGGAGAGACTGATAGGACATAGCTTTTCTTGCTTGGTGCTGGTGCATTAGCTTTGCTAGTTGGTGTCTGATCTGAAGCAGAACTGATAGTATACCTTGTTGGTGTCGATGGACTATCCATTGGTAACATACTTTCTGTCGTTTGTGCTTCTATCTTTGATCCTGTACTGCCTTCACTTGTTGCTGGTGCTAGTTGGAGAGAGCTGCTTGAGTCTGCTGGCATAATAGCTAATGTCTGTTGTGAACTGCTTGGTGAGATAGGCAGTAGGCCCTGCACTTCAGCATTGGATGAGATAATGTTGTTAACCTGTAAGGTTTCTTGATTTTTCATAATAGTATCTTGTGTGAAGCTGATGTTCCAGATAAAGGTTTGGTTGAAAAGAGCTACAATCTCATCTGGAATATATTCACTGTCAGGTGGATTTTGGTCAATGAGAGTCTCAACCGGTTTGCGTACGAGGCGTTGTGCTATTCTCCCAAAGAGGATAAATGTAGCTTGAGCAGTATCATCAGCAGCGATCAACACAACCTTGTATCTTGGCACTGGTATGCCTACATTGGAGCAGCTGGTGCATTTATAGGTGGAACCATATGGTTTTGAGGTCTTGTAGCATATGTCACATGAATAATACCACCAGGAGCTGTTGCTTGATATGCCTTTAATAGTCACTCTGACTATAAAACGTGCTCGCGCATGTTTGTGTGGGTTGAGAGCAAGGATTTGTGCTATGGTTTTTTCTTCTGGAATATCCTGGTTAAACCCTGTGGTAGCAGTTCAACCCACTTGATAGGTTGAAAGTTTGCGCTAAAGCTTTCTTTTAACTCAAGCACTTCAGGCATATCAAGGTTAATCTACCATTTGCATGGTGAACTTCCATTTAAAGTTAGTCCTATCCCTTTGTAGTTCTTGACAACTGTTCCAACAAAAACAATAACCTGAGGTTTCTTTTGACCAGCATTGTATAATTCTTCTGCATTGAATGCAGCTGCAGTATTTCCCCATAGTGTGATAGGCAGTGTAGAATTGCTAGTTTTATAAAATGATTATAAATTTTTGGTGATCAATATTAGTAACTTGTTACAATAGTTAGTGTGGATAATGTAAGGTAAAGGCAGTTTATAACAAAAGAAAATTTCAGTCTATACTGTAGCTTACCTTGCATCCCAAATCTGCATTGTTCTTTTCAAAGTTTCTGTGTTTCTTGATTTTGGGCGTAGAGTGTCTGTTGCACCAATTTCAGTTATGACACCCATAATATCAACATAGAAAGCATTTTTGTCCACAAGAGACGGGACGTCTTGAAAAGGTGTCAATGAAAAAGTTATGGCAGGGAAATCATCAGAAGCATCAATGCATTCTTCTAAGGTTGTCCATTTAGTGAATGAGATCATCAAAGGGTTCGTAACTGGCCTATATGTTCAGTTTGCATATCTGACAGAGAAGGAGTCAAAGTAGTAAACCTTCCCTTCCTGTAGAAGAGTCCTAAGCTTAATCATGGCAGGTGGATAGATTTGAACATGGATGCTATTGCCCTTTTCATCCAGCAAGACAAGATCAGTGTGGAAGATTTTTGTTTCATCATTCAGATCATGGTAGTCCCATTGCCTAGATACTCTTGCCTTGAACTGTTTATTAGTGTCCCCATACATAAGGTCTGAAATAAGCACGTATACCATTGGAAGCCCAATTTGCAGAACTATCAAGCCGCTTCAACAGTTTAACAACTGCAGCACTAATATATCACTTACATAACAGCAAAACTGCCCTGCTGAAAGCTCAGAATGAGATATGTCACTCCGAAGCAACAACAGAAAAAGAATGTTAAAAGGAGTTTATATATAAAAACAAATGCCTAATTAAAGTGCAAAATTAGTCCATTTGGAAGCCTTCA

Coding Potentia
Explanation CPC Score
noncoding -1.02152
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0390700.2 7 26720392 A G
Osa07LNT0390700.2 7 26721156 C T
Osa07LNT0390700.2 7 26722144 C T
Osa07LNT0390700.2 7 26722467 C T
Osa07LNT0390700.2 7 26722519 C A
Osa07LNT0390700.2 7 26722540 A G
Osa07LNT0390700.2 7 26722914 G A
Osa07LNT0390700.2 7 26723461 A C
Osa07LNT0390700.2 7 26720833 A T
Osa07LNT0390700.2 7 26720267 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
Osa07LNT0390700.2 osa-miR5826 Cleavage 5.0 21.395 1 24
Osa07LNT0390700.2 osa-miR1861o Cleavage 2.5 14.938 1 22
Osa07LNT0390700.2 osa-miR164a Translation 5.0 15.041 1 21
Osa07LNT0390700.2 osa-miR164b Translation 5.0 15.041 1 21
Osa07LNT0390700.2 osa-miR393a Cleavage 4.5 11.468 1 21
Osa07LNT0390700.2 osa-miR164c Translation 5.0 15.041 1 21
Osa07LNT0390700.2 osa-miR393b-5p Cleavage 4.5 11.468 1 22
Osa07LNT0390700.2 osa-miR164f Translation 5.0 15.041 1 21
Osa07LNT0390700.2 osa-miR1435 Cleavage 5.0 22.447 1 20
Osa07LNT0390700.2 osa-miR1861a Cleavage 2.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861b Cleavage 3.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861c Translation 5.0 14.938 1 22
Osa07LNT0390700.2 osa-miR1861d Cleavage 3.0 14.938 1 22
Osa07LNT0390700.2 osa-miR1861e Translation 4.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861f Cleavage 3.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861h Cleavage 4.0 14.938 1 22
Osa07LNT0390700.2 osa-miR1861i Cleavage 3.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861j Cleavage 4.0 14.938 1 22
Osa07LNT0390700.2 osa-miR1861k Translation 4.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861l Cleavage 3.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861m Translation 4.5 14.938 1 22
Osa07LNT0390700.2 osa-miR1861n Translation 5.0 14.938 1 22
Osa07LNT0390700.2 osa-miR1862e Cleavage 4.5 21.923 1 24
Osa07LNT0390700.2 osa-miR2873a Cleavage 4.5 12.313 1 24
Osa07LNT0390700.2 osa-miR2873a Cleavage 5.0 19.908 1 24
Osa07LNT0390700.2 osa-miR5083 Translation 5.0 15.507 1 20
Osa07LNT0390700.2 osa-miR5149 Cleavage 5.0 19.967 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0390700.2 7 nan Physiological trait Eating quality R1245 R1789
Osa07LNT0390700.2 7 qPLLN7 Physiological trait Sterility RM234 RM172
Osa07LNT0390700.2 7 nan Resistance or Tolerance Other soil stress tolerance R1245 R1789
Osa07LNT0390700.2 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0390700.2 7 hd7a Physiological trait Flowering RM18 R1789
Osa07LNT0390700.2 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
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