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

>Osa12LNT0137800.4

CTTACTAAACATATAAAATGTTGTACGTACTCTTGCCACCTTTGAACAATGTGGGAGCATGAGAAGCTAACAAAATAGGATTAGATAAGAACAATAGATGTAATATATTTGGATGGTTCACAAGAATTCAAATACATGAATTTTAGAAGAAATCCTATGTAGAAAAGAAAGCAGAGAGAGAGGAAAAATAAAAAAATAAAACAAGAGATATGAGCTCATGTTATACTTCTTATGGAATGAAGTGTATAGGGAAGCAATCCATAGTAACCTTGCAATACTATTCCTTTGGTACAAAGGGTGTCACAGTAATTTTTTTCACCAAGGATTCCAATACTTAAAAGTAATTATATGGGCTCCTTTGAATCACAGGATTGAAAAAAAAATGGAGAATTAGGAAAAATATAGGATTCTGATATAAATATAAATATAAAATAGAGGATTGGAAAATACATGAAAAAAATATAGGAATGACCGTTTGGTTGGGCCGCAATAAAAACACATGAATTTTGGGAGAGATAAAGAGTCAAAGGATTCTTTCCATGATGTTCTACCTTATGTTAAATTTCCTTCAAAAATTTATGGGAAGAAGCATTCCATATGAATTTCATAGGATTTATTCCTTTGATTCAAAAGCTATATACGAAAAGTTCCTATAAGAATGAAATCCTTTAAAATTCATATGAATTTCCTTTCAATCAAAGGGGCTAAGAATTTCTTCTATCCAAAAGATCTTGTAATACTTCTACATTTGCACGATCCTTTTTCATAAATTTGTATTAACTACTGGACCTAAGTGGAAAAAAGTCCATAGGGGTGAGACCGTGAGAGTACACCCCTGCCCTGACGTCCTGACCCCACCACGGCTTTCATCAAAAACCCGCCGCCGGCGCCGCCGCCGGCACATTCTCCGGCATCCTCCGGCCATTTCCGGTCACTCTCATAGCCTCCAAATATAACTTTGTCAAATTTACAGATCAATGTAGACACGCGATCCATCACGGGCTAACTGCACATCTATCCCCTCCCTTCTGGACCACTCTTCCAACGTTTCATTGTCCTTGTGATGGTCCATTTCATCAGTCATCCCAATGAGCAATGCCCTTTTGGGGCAAATCCTCTTAACAGCATCCAGTGTCTGATCCCAACAAAGATGGACATTATGAGAACCAGTCCTACTAAGGCAATCCAAGATGAGCAAATCCAGCTGACCCCCTCCAGACTTTGAAATTGCATGTTCTGTGCTTGGAGGAAACCATGAAACGTCTGATATATAAGCAACTTTTGATTTTCTTCCAAAAAGGAAACCCAGACAAATGTAGTCCTCGCCATGGATCACTGGAAGGGGAACAAACTCTAGCCCTGAGGTCACAAATGGTATCTGAAGATCACTCTCGATTACTCTCCAGTCAAGCTGAGCAACTCGCCGAACCTCCTCCCCTTCCTTTAGTTTCTTTCTGACCAAGTAAGGAAACTTTTGGGCAATGCTGTCCATAGCAAATTGGGATAGATAAATTGGAGTTGGTTCAATATCATTCGTAGGACTAAATGACTGTACAATCCGAACATCATCAAGACCCAAGATTGCATCAGCATGCTCATGAGTCAGAATAATAGAATCAACACAAGGGATTTTATGATGGACAAACCACCGTAGAACTTGTTCTCGGAATGTCTTCCCAACATCAATTAGAATATATTTGTGTGCATTTTCATCTTGGCAATAGTCAATCAGAAGAGAAGTATTGCACCTGTAGTTAGGGTTTAGCTCGGGGGCCACGGAGAGGGACTGGGAGCAGACGGCGCAGGGCGGGTCGGGGGGCTGGATCAGGCACCGCGCGTTGGGCACGGCGCTGGAGCAGCCCGTCCCGAGGAACACCAGCGAGGATGAGGAGGACGGCGGCGGCGGCGGTGGCGTCCCTCCTTCGCCGGTGGCGGTGGCGGCGCCGTGTCCGTTGGGGACGGAGGAGGCCATTGGCGGCGAGACGAGGCCTCTCTCCGCCGGCGACCGTGGCGACGACGACGAACGGCGACGGCGAGTCGGTGAGGGGGAGGAAAGAG

Coding Potentia
Explanation CPC Score
noncoding -1.0522
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0137800.4 12 26110245 C T
Osa12LNT0137800.4 12 26112196 G T
Osa12LNT0137800.4 12 26112463 T C
Osa12LNT0137800.4 12 26113783 A T
Osa12LNT0137800.4 12 26114386 G A
Osa12LNT0137800.4 12 26114395 G T
Osa12LNT0137800.4 12 26114485 A G
Osa12LNT0137800.4 12 26115331 T C
Osa12LNT0137800.4 12 26115509 A G
Osa12LNT0137800.4 12 26113693 T C
Osa12LNT0137800.4 12 26115768 A G
Osa12LNT0137800.4 12 26112571 T A
Osa12LNT0137800.4 12 26111486 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
Osa12LNT0137800.4 osa-miR812s Cleavage 5.0 15.245 1 24
Osa12LNT0137800.4 osa-miR5807 Cleavage 4.0 16.094 1 24
Osa12LNT0137800.4 osa-miR5079b Cleavage 4.5 16.969 1 22
Osa12LNT0137800.4 osa-miR393a Cleavage 4.5 15.898 1 21
Osa12LNT0137800.4 osa-miR159f Cleavage 4.5 15.746 1 21
Osa12LNT0137800.4 osa-miR393b-5p Cleavage 4.5 15.898 1 22
Osa12LNT0137800.4 osa-miR396e-3p Translation 4.0 13.528 1 24
Osa12LNT0137800.4 osa-miR812a Translation 4.5 15.208 1 22
Osa12LNT0137800.4 osa-miR812b Translation 4.5 15.208 1 22
Osa12LNT0137800.4 osa-miR812c Translation 4.5 15.208 1 22
Osa12LNT0137800.4 osa-miR812d Translation 4.5 15.208 1 22
Osa12LNT0137800.4 osa-miR812e Translation 4.5 15.208 1 22
Osa12LNT0137800.4 osa-miR1850.1 Cleavage 3.5 14.199 1 21
Osa12LNT0137800.4 osa-miR1859 Translation 5.0 17.616 1 22
Osa12LNT0137800.4 osa-miR1866-3p Translation 4.5 22.39 1 22
Osa12LNT0137800.4 osa-miR1862d Cleavage 4.5 12.932 1 24
Osa12LNT0137800.4 osa-miR1862e Cleavage 3.0 12.693 1 24
Osa12LNT0137800.4 osa-miR2095-3p Translation 5.0 19.313 1 20
Osa12LNT0137800.4 osa-miR5079a Cleavage 4.5 16.969 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0137800.4 12 qLEI 4 Resistance or Tolerance Submergency tolerance RM5479 C901
Osa12LNT0137800.4 12 nan Resistance or Tolerance Submergency tolerance R1709 RM235
Osa12LNT0137800.4 12 nan Resistance or Tolerance Submergency tolerance RM5479 RM6953
Osa12LNT0137800.4 12 qSD12 Physiological trait Germination/dormancy RM3331 RM235
Osa12LNT0137800.4 12 qLEI12 Resistance or Tolerance Submergency tolerance nan nan
Osa12LNT0137800.4 12 qNEI12 Resistance or Tolerance Submergency tolerance nan nan
Osa12LNT0137800.4 12 qTIL12 Resistance or Tolerance Submergency tolerance nan nan
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