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

>Osa06LNT0362500.1

CAATCAATCCATGGATGATGATTTTTGTTTGCTCACCTCTGCGGCCCATACATAGGCCATAGCCGGTTAGCTACTATACAGGTTGCTCTTTCTTCAGAGTCATACATACATATGTGCTGTAGCATCAAGGAAGGATATACATACATGATGTGAAGGAAATATTCAACCATCACCTAGCCTGCCTGCCTGCCTGCAGCATTTTCCCTATACATGCTATGTATGATACACACAATAATATAATTTCCTCAACATTAATCGGAAGGCAGATGCTGTCTGATTTTTCCTATCTAAGCCTAACCTGCTCATCATCTTCCCTTTATCTCCTCTTCCCGCCTCCTACTTCTGGCTATTTCTCAGTGAGTAGGGCATCAGCAATGATCTACCATATGCAACTGGAAGCGCTAGCAATTTCTTCGCCTTCCCAACGTACGCCCTCTTTGTGAAGTTGTTGTAATCGTTTGCTTCTATCTCGTCAAGGATTTGCCGGTATAACAACAGAGACGCCCAGACCGGCCACCGGCTTGCCTGGCTGAGCTCGGTCACCCCTCTCTCTGCCTCCTCAAAAAACATCCTAGCTCTCTTGATCTGTCTCTTCATGAAGCTTCTCCATTTGTTAGTCACAACGCCATTGAAGATGTCCTCATCAGAGAGCCCTGCCTCTGCAAGTTCATCTTGTGGTAAATATATCCTCCCTCTTCTCGCGTCCTCTCCAACGTCACGGAGTATATTTGTGAGCTGGTTTGCAATGCCGAGAGCCAAAGCAGCACTGTACACACTTTCAGTTGTTGCCTTCGACTCGGGTGCAATACCCATCACAGGAACACTCATTAGCCCCACAGTTCCAGCAACATAGTAGCAGTACATGTAGAGCTCGTCGAAGTTCTTGTATCTAGTCTTTCTGAGGTCTGACCGCATCCCTTCTATCATGTCCCTGAAAGGCTGAATATCTATAGGAAACTTGGAGATGGTATCAGAAAGTGCAGCATCAAGCATGTCGTAGGGGCGTCCGGTGAAGAGATCATCAAGCCTCTTCTCCCACCGGTCCAGGGCTGACGGTGTGATGTGCGAGGCATTTGGTCCATCTACAAGCTCATCTGTCCTCCTACACCACACATAGATGGCCCATATGGCGCGCCGTCGGTCCTCCGTCATGAGCATAGTTCCAAGGTAAAAGGTCTTGGCATACTCCTCGCAGATCTCTCCGCAGCGATGATAGGCCTGCTTGAGGCCGTTTCTTGGCAGGTCCAGGTCCTTGGGAACGATGGGAATGGTGTGTGGTTGTGGGCGCAGGTGGCGTTTGAGCAATGCTGCCTGCTTGAGGACGACGTCGTACACCTTCTGCTCCGAGGAGATGACGGCCTCTCCAGCAGGGGTGACGGTGAGGCTGGAGTACACCGGCGAGGTCCGGGCAATCTCGCCCGGGGCAGGGTCGACGCCAAGGCAGGCGTACTTGAGCGAGCAGAGGATCCACCTCCTCTTCTTCTCCTTGTTGTTGGGCAGGTAGGAGGAGCAGACATGTTGGACGGCAGCAGCGTCCCGGGCGAGGGCGTCGGAGAGGCCCGGAAGAGACGCTGAACGTAGGAGCGTGATGGCCGCCATTATTATACTGGATGGGATCAATCGCTGGCCGGAGATCGATCTGCAAGGTAGCTAGAATAGCGGGGCGTGTGTGCTGTGTGTATGTATCAGTATCAGGCAGGCAGGCAGGCATTCAGGCGCGCACACGTATGGTATGCAGTGGCAGAGGATGAGGAGTTTGGCAGGCAAAAGGCAAGGTTGGAATGAGTTGGAGGAAACAATTACCTCTTATCACTCTAGCTAGCTTGTTCTTCTTCTACCAGCACCAGGAAGGAATGAAGGAAAGGATATGCTGGTGCTTGGTTGCAGCTCAGCATCGATCATCAAGCAATGATGCTAGTGACAAAGTCGAGAGTCTGCGTGTAGTGTCGGGATGCCTGGTCTGGTCTGTGTGGAAGGAAGGAAGGAAGGAAGGAAGAGAGGGTGGATGATGAGCTATGGCTAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.966093
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0362500.1 6 31054504 G A
Osa06LNT0362500.1 6 31054561 T C
Osa06LNT0362500.1 6 31054633 G A
Osa06LNT0362500.1 6 31055250 C T
Osa06LNT0362500.1 6 31052944 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
Osa06LNT0362500.1 osa-miR5789 Cleavage 4.5 21.503 1 21
Osa06LNT0362500.1 osa-miR5803 Translation 4.5 19.566 1 24
Osa06LNT0362500.1 osa-miR160a-5p Translation 4.5 23.56 1 21
Osa06LNT0362500.1 osa-miR160b-5p Translation 4.5 23.56 1 21
Osa06LNT0362500.1 osa-miR160c-5p Translation 4.5 23.56 1 21
Osa06LNT0362500.1 osa-miR160d-5p Translation 4.5 23.56 1 21
Osa06LNT0362500.1 osa-miR160e-5p Translation 4.5 23.56 1 21
Osa06LNT0362500.1 osa-miR171g Translation 5.0 16.069 1 21
Osa06LNT0362500.1 osa-miR1860-5p Cleavage 4.5 22.03 1 21
Osa06LNT0362500.1 osa-miR3980a-5p Cleavage 5.0 24.66 1 21
Osa06LNT0362500.1 osa-miR3980b-5p Cleavage 5.0 24.66 1 21
Osa06LNT0362500.1 osa-miR5493 Cleavage 5.0 21.454 1 21
Osa06LNT0362500.1 osa-miR5523 Translation 5.0 16.89 1 22
Osa06LNT0362500.1 osa-miR1857-5p Translation 5.0 17.65 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0362500.1 6 qREP-6 Resistance or Tolerance Other soil stress tolerance nan nan
Osa06LNT0362500.1 6 nan Morphological trait Root RM5814 RM3509
Osa06LNT0362500.1 6 nan Morphological trait Root RM5814 RM3509
Osa06LNT0362500.1 6 nan Morphological trait Root RG653 RG433
Osa06LNT0362500.1 6 nan Morphological trait Root RM5814 RM3509
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