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

>Osa12LNT0130700.2

ATCTGCAAATGGGTCTTTTAGAATTCAGAGAAAGGGATAACATTACATTTATATAATCTGACACAAACTTAAAATCACAAATCCACAAACTATCTTAGTTTGTTCCTTTTTTCCCCTTATGTACAGCTCCATCCAAATGGAAATTTCATGAATGGAGTTTCATTCCATGTTGGCATGATCTGCTTCCTGGAGACCTGGACTGAAGTCCCCCCCTGCATTGCTGCCTGAACTTCTTTGTTTTCTGACAGCAAGAGTGGTTTGCGCTTGCAAACACCAAATTAAGGCAAGAGATGAAAGGATTTGAATCAATCACTTGGTGCTCCTGTGACCTGATGAAGCCATGAGCACCGCGACCGCGACGATGAACATGAACAGCATGAACCCGAGCAGGATATACGTCTTTCGCGACGATTTCCGGTACTCCCCAAACAGGAGTATTCCCCAGAATGTGCTCACAAGTGGCAATGCCTGGACAGCATCAGCAGCAGCATAGCCAGCAGCCTGACCACCCATGAACTGAAACCCATTGCCAAAGCCACATAGGAAGCCAGCCAGGAGAGCCCACTGCCTGCCTTCCCAGTCATTCAGGTAAGCCTTGAAGGATGATTTCGGCACACCGGCCATTGGACGGTAGAGGAACAGGATGTTCAGGCCGATGCCGATGACGAAGCACGAGATCGAGAAGTAGAAGAAGGCGGTGTACACCACCAGGTGTGGTACACCTTGTTTCAGGGTGTGCCATTGGTCATTGGTGGCGAGGTTGAATGCCGGGGAGAAGAGTGAGAAGCAGACTCCTGAGAAGAACACTATCCCAAGCCCTATGAAGGTGCTTGATCCGAACACCTTGATCGAACGCCGTTCTTCGAGCTCAATCAAGTATTCCGCAGTTCCTGCTTCAGCTTTGGCAACATATTTGGTTGCAGAAGCTCCATTCTCCAAGTCCTTGGGAGCATCTTTTTCTATGACTTCTTTGTTTGGTTCCACACTTCCATTTTCCCCAAGTTTATAGATATTTGTGGAGCCATTTAGTTTTTCTTCATTATCAGCTGCATTGGAGGCATGTACAGCAGAGCCAAGAATGACTGCAACAAGGAAGCAGGCCACTCCAGGGAAAAGAATCTCTGCTCTGTTGATGCGGTTGTCCAGGAAATAATTCAGTGTTGTGCCTATTACAACAACCATACTTGAGCTGATGACCTCAGTCACTGAGAGACCTACATATGCCCATGCATACTGAGTAGAGAGGTTCCCTATACTGAGCACAACACCCCCTGCCATTGCAAACAGCACTGAAGGCCAATTATCCTGACTGAGCTGGGTGAAGAAATTGGGCATGTTGGGCTTGCTATCGCCGAGCTGACCGAAGGTGAGCGCGATGAGGACCGCAGCGAGGAGGTTCGTGATCGAGTAGTCGAGGTAGGTGTGCTGCGGGAGCCGGCCTCGGCGCTCGAGGAGGGTGAGGACCGCAGGCCATGTCCCCAGGAAGAAGAGGGAGGCCAGCATGAGGGCAATGGCACCCCCTTTGTCCTCTATGATGTACATCTTGAGGCCTCCTTGTCTGATGGACAACAGGGAATTCACAAGGGGGCCTTCAAAAACCTAAAGTCAGAAGGAGAGAAAGGGATGAACTGCTCCTCCTCCAGAGAACTCAAGAACTGAACTCTCAAGTCTCAACAGCCTTTGTCACTGCATAGAATTCTTCAGGTTAAATAGATAGGCAGCTGGGGTTTGTTGGACTCTCTCTACTACTACTCACTCCTCCAGCTGACACGCAAGAAGGGAAGGAATTAACCATCAAGAGATTCTTGTTCTTCTCTCAAGAGGGCCAACAAAAAAAAGGGAAGAAGATTCTTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.543681
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0130700.2 12 19162421 T G
Osa12LNT0130700.2 12 19161993 A G
Osa12LNT0130700.2 12 19162016 C A
Osa12LNT0130700.2 12 19162056 T G
Osa12LNT0130700.2 12 19162357 G A
Osa12LNT0130700.2 12 19162559 A G
Osa12LNT0130700.2 12 19162560 T C
Osa12LNT0130700.2 12 19163027 C T
Osa12LNT0130700.2 12 19163068 T A
Osa12LNT0130700.2 12 19163446 C A
Osa12LNT0130700.2 12 19163915 G A
Osa12LNT0130700.2 12 19164948 G A
Osa12LNT0130700.2 12 19165020 T C
Osa12LNT0130700.2 12 19165084 A C
Osa12LNT0130700.2 12 19165251 T C
Osa12LNT0130700.2 12 19165258 A G
Osa12LNT0130700.2 12 19165546 C T
Osa12LNT0130700.2 12 19165621 T G
Osa12LNT0130700.2 12 19165846 C T
Osa12LNT0130700.2 12 19165950 A T
Osa12LNT0130700.2 12 19166293 A G
Osa12LNT0130700.2 12 19164921 C G
Osa12LNT0130700.2 12 19161949 A T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0130700.2 osa-miR5798 Translation 5.0 22.034 1 21
Osa12LNT0130700.2 osa-miR6245 Translation 4.5 19.068 1 21
Osa12LNT0130700.2 osa-miR156c-3p Translation 4.5 21.224 1 22
Osa12LNT0130700.2 osa-miR156g-3p Translation 4.5 21.224 1 22
Osa12LNT0130700.2 osa-miR160a-5p Translation 5.0 15.717 1 21
Osa12LNT0130700.2 osa-miR160b-5p Translation 5.0 15.717 1 21
Osa12LNT0130700.2 osa-miR160c-5p Translation 5.0 15.717 1 21
Osa12LNT0130700.2 osa-miR160d-5p Translation 5.0 15.717 1 21
Osa12LNT0130700.2 osa-miR160e-5p Translation 5.0 15.717 1 21
Osa12LNT0130700.2 osa-miR167d-3p Cleavage 4.5 20.059 1 22
Osa12LNT0130700.2 osa-miR171d-5p Cleavage 5.0 17.756 1 21
Osa12LNT0130700.2 osa-miR1861b Cleavage 4.5 18.771 1 22
Osa12LNT0130700.2 osa-miR1861f Cleavage 4.5 18.771 1 22
Osa12LNT0130700.2 osa-miR1861h Cleavage 5.0 18.771 1 22
Osa12LNT0130700.2 osa-miR1861i Cleavage 4.5 18.771 1 22
Osa12LNT0130700.2 osa-miR1861j Cleavage 5.0 18.771 1 22
Osa12LNT0130700.2 osa-miR1861l Cleavage 4.5 18.771 1 22
Osa12LNT0130700.2 osa-miR5077 Translation 5.0 23.066 1 19
Osa12LNT0130700.2 osa-miR5489 Cleavage 4.5 14.877 1 21
Osa12LNT0130700.2 osa-miR1430 Translation 5.0 20.759 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0130700.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0130700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130700.2 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0130700.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
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