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

>Osa05LNT0322000.2

GCTTTGGGACCGCTCCCTCTTTCTTTCTCTCTCTCACTTTAGTGCTAGAATGGAAAAAGTTTAGGATGCATCTAAATACCAACTAGTACTTTTGCAATACCAAAACTTTTGCCATTTGCCATTTGTTATTTCAAATGGATCTAAACAGGGCCTTAATCTTCAGAGAATGCACATTTTACCTCTCTCACAAACCGGTTCATTCCGATCATGCAACACATTGCTTTTCTGTGTTTGGTTCTTTCTTTCAAATCGATCGCTGCACAGATCCAAACTAAAGCGCGAAGGCTGCAGGGTTCAGAGGAGAAAGACGAGAGGAGGCAAAGAAAAGAGGAGAGGAGAGGCTGGCTGCTGAACCAGCACAGTTTTTGCTTTCCTCGGGATCGGTGGCAATGCAAAGCGGGGCCCAAAGGGGGGTAAAATCCAAAGCGAAAGCTGCAGCTTTGACCGCGGAGGGGGCCGACCGACCGGTGCCGACGGCGACGGTGCGTGGCGACGGAAGCAGCGCCCTGCAGCGCCGGAGTGGCCGGGTCCAGGTGACGACGCGACACACCGTACTAGCGACCTCATCGTCGTCGTCGTCGTCCCCGGCTAGTGCCAGTGCTACAACATGCTACCGCTAGGAGAGAGAGAGAGACACACACACAGGCCACAGCTACTCTACATCTGTCTCCTCTCGAGCTTAGTACTGTTGCTGGTCTGGTCTTATGGCCTCTGCCTCTCTTGAGAAGATCAAATCACGCTTAAATTCACCTCTTCTCCTTCGTTCCTAGCTGTAGCATGTTGCTGTTCCTGTGGTCTCCACAGCAGGGTTTCTCAAATCGCCGGGGCTAGGGTTACCGCACCCCAGCGGTAAGCACGGTTACCGCGCGATAACCGTAAAAACCATGCAAAATTCATCAAAAATTCAAATTATTTTTTAAGTTTATTTGAATTTAAGAAGGTTATCGTGGTTTTTCTACTACCGTATCCTGGGATAAGACCGGTAACCGTGCTGGTAATGTAAACCCTGCTCCACAGCTCGCAGGCGCAGCTCAGGGCTCAGGAGAGACGAGGGAGGGGGAAAGGAATTTTCAACGTGTTCCAAAGGCATGTTCATTGTTCAAACCTAGTTTGTCCGGTTCAGCATTAACAAATCTTCTGAAGCGCAGCTTAATTGTGCATGCACATTTAGCAACAGGTCAATGTGGCCTGGAACCTATCCGTATGCAGCCCTCTTCAGAAGGGACTAATTCGGTGTGCCAGCTTTATTTGCCACTCAGAAACCAGCCGGCCTGGGATAGGTGCCAATGCATCCTTCTCACGTGCATCTGCATCATCAGCATGGATAACAGAAATAACGTCTTCAACCAGTTTGTCCCTGCCACCCCTTAGTGGATCCTGTAAAAATACATCAGTATGTGTTTTCCCTTCATAGAGTAGTAACTTGGCTTTAGCACCAGCTTGTTTAAGGACACCCGCAAAAGTTTCACTAGCAGAAAATGGTATAGAATAATCATCCGTTCCATGCAAAAGCACAATCTGAGGAAGAAGAGCTATTGTTTCAGGACATAATTTCTTGGCAACAGTTTCTGGAGAGAAATGTGGCAATGATTTCTTTCCCTCCATTATGCTGAGAAATATTGAACGGTAAAGACCACGTTCATGGAAATGATCAACCAAATTTTCAATGTTGTATCCTCCAGACAAACCAAAGTATGCTTTTATTTGAGTAACACTCCATGAAATCTGCTCTCCCCTAGATTCTTTAGCCGCTTGTTCCAAAAGAGCGCATGCTGCGATATGTGCTCCTGCTGATTGACCCATTAAGTATATCTGATTAGGATCTCCTCCATAGGCACCAACAGTCTCACAAACAAATGAAATCCCATCAGAAGCATCGCTAACCATGTCACTTATTGTTCCTTGAGGAAAATTCCTGTAATCAATGCATGCAACTATAATTCCTCGCTCTGCTAACCTCCTTCCAAGAAGAGCACCCCACGCCTTGTAACCAATGATCCATGCACCACCAGTAACAAATGCAACAACTGGACTGGGTTTTTTGGGGTCTCTTGGTATGTAAAGATCCAACCTATTTCTTGGTTGATCCCCATAGATCACGCTCCTCAAAACTTGTCTTGAAAAGAAATAATAATACCCAACTCTTATGAAACCGGGCATAAGTAAAATTGCATATATTATGAGGGCAGCGAGCTGAGAAATCCACCGGTAGCCTACCCCGAGGTATCGGAGGAGGATGAAGGCGAGGCGCGTGACGAGGTACGTCTCGGCGGCGGCATGGCTGACGTCCTCCCGGAACGTGGACCTCCTCTCGCCGCCCCCGCGGCTGCCGGGGGCGAGCGGAGAGTCGGGGGAGAAGGGCACGGAACGCCGGCGCACGAGGACCTGGGGGGCACCGCGTGGAGGTACCGCCTCCGCCACGGGGCCCGCGTCACCGGAGACCGGACTCGCGGGCTGCATTGCGGGGCGGACGACGACGACGATGCTAGCTCCTGGTGGCGAGGGATTTGGGGTTGCCGC

Coding Potentia
Explanation CPC Score
noncoding -1.13309
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0322000.2 5 28745923 C T
Osa05LNT0322000.2 5 28746045 C A
Osa05LNT0322000.2 5 28746620 C T
Osa05LNT0322000.2 5 28749332 G A
Osa05LNT0322000.2 5 28749975 C T
Osa05LNT0322000.2 5 28750867 T A
Osa05LNT0322000.2 5 28747999 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
Osa05LNT0322000.2 osa-miR5817 Cleavage 4.0 19.862 1 24
Osa05LNT0322000.2 osa-miR5512b Translation 5.0 14.149 1 21
Osa05LNT0322000.2 osa-miR1320-5p Translation 4.5 12.124 1 21
Osa05LNT0322000.2 osa-miR5160 Translation 5.0 20.556 1 22
Osa05LNT0322000.2 osa-miR5512a Translation 5.0 14.149 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0322000.2 5 qRNw5 Resistance or Tolerance Other soil stress tolerance C1447 RM26
Osa05LNT0322000.2 5 qRSd5 Resistance or Tolerance Other soil stress tolerance C1447 RM26
Osa05LNT0322000.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0322000.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0322000.2 5 nan Physiological trait Eating quality C246 C1447
Osa05LNT0322000.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0322000.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0322000.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0322000.2 5 tp5b Morphological trait Culm/leaf RM26 C1447
Osa05LNT0322000.2 5 qMRL5-1 Morphological trait Shoot/Seedling RM26 C1447
Osa05LNT0322000.2 5 qTDW5-1 Morphological trait Shoot/Seedling RM26 C1447
Osa05LNT0322000.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
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