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

>Osa12LNT0130500.1

GACATTCGCATGTGGTAAGTCAATCTGTGCCCTCCAAACAATATTACAAGCATATATAGTAGTTGCCAATGTACCCCACGCATTTAAATTCTAGTGATTAGCAAGTGACATTAACACCTAGAACACTGAGTACAACCACAAACTAGGTTCCCAGGTTCCAAAATCGATTTGTCCACAAATTTAAGAAATGAAGATGGTAACTGCATGCACTGTTGTCCTATCTTTGACACCATTTGATCTTCACCTAATAATATTAGCTCCATGACCTCACAAAAGCACCCAATCTCATGTAAATCAACCCATCTGAAGTTTCAGCCACAAAATTCTAGCGGTTGGATTAGCACTGATAAAGATTTCTCTGTTCTGAGCATCCTTAAAAACACTAAATGACCGGGCATTTTCCTCAGGGGATAGTTCATTCATTGTGCTCAAGACATCGATACATTTCTTGATTGAAAATTCATCAACTTGCTTTGTAGCCTCTTTTTCCCGTACCATTTCCTCCTCAGCTTGTTTATGTCACAGCTCTATGTATTTCTCCATTGCATCAGCCACATTCCCATTTTGCTTATGTCTTTTTGGGTTCTTCTCTCTTTTATCCTCAGGAGGTTTCCTTGATGTACTGACAGTTTGTCTTCTTTGATTTAACTGATTTGACACTTCAACTTTTGATTGTTCACTTGCTGTGATTGGATCATCATTGTTTAGGTCATCTTGATTGTTCTCCATCAGCAAATCATCAGCACCTACTTGTGTAACAATATCATCTTCTGTGTTTCTTGACTGATCTAGTGTATTTGTTGGCTGAAGGGATGTAAAGTTCAAGAGGCCCTCGGCAGTTTGACCATCATATAGTTCTCCTAAAGCTTCAAAGATTGGAAATGGTTTGTTGCGGAACTTCTTAGCTCGAGGGAAAGAATGAATAATATTATCCCAAACTGCAGGATCATCAGCAATAATCATCCCGAGTTTTTCGTCCCAAGATGCCCCACTTTGTGTTCTTGCATCTTTCAAGCACCTGTAGTCTCTCTTAAGCTCCTTTTCTTTATCTTGAATTTGTCCTTTTGAAAAACAAATGTGCGGGAACTTATCATGAAAACACACAAGTCATTTATTACATCACATTTCATTACATATCATGCTAGATTAGAATGATCATGAACATAATCATTCCACATCGCCATTGCAATATTGTCCCTAATAACATTTCCTTGATGAGTTTGATTATTCAGTGAGTTGACATCATTGCCATACTCATCACCTCCCGCTGGAACATCAACAAAATCTTCAGGTGATATATGGTGTGGATCATGTGGCTGATGATCAAGATCCAACCATCCCTCATTCCCATTGTACCTCCTAATCAGGTTGTGAAATACGGCAGCAGCTGCTGGTATCCTAACTTGGTTTTCAATAGGGTGTAGTGTGCCTACTTTTAAGATCGGGAAGCGCTTCTTCAAAACTCCAATAGCCCTTTCTATGTGATTACGCAATAATGCATGGCTTTGATTGAACAATTATTTGTAGTTTGATGGGCGCCGGTGACCACGACCAAACTCCTTAAGATGGTATCGAACGCCACGGTAAGGTGCGAGGAATGAAGGCGTGTTGGCATATCCACCATCAACAAGGTAAAACTTGCCCATCGGTATGCGAAAACCATTTAGTTGAGCAGACCTAAGCACCCGGGCATCCGTGGCAGATCCCTCCCAGCCACAAGAAATGAATGTGAAGTTTAAGTCAAAATCACATGCTAACATCACATTTTGGCTTAGTGTGCTCTTTCTATTCCTATATGGAGCTGCCATCTCAGGGTTTATAGTGATAGGAACATGAGTACCATCAATTGCTCCTAAGCAATTCTTGAAGTATGGGTAGAAGCGAGGATTTGATGTGATCTTTGAATGAGTTTGGTTTGCAAGAGGCGGCTTAATGAATCTATGGGTGAGAGTAGGGACTATATCGAAAAATGCCCTAATATGTAGGTGGATTGTCGCCCCACTATGCTTGAATTCATATTGCATATCTTGGTAGCTCGCATTATGGGATAGCATATACATGAACATAGCAAGCTTTTCCTCCACTCTAACTCCCCTAGTGTCACGGACCAAGTTCTTCCTTCTTAGAAATTCTGCAGTACTTTTGAAGACCTCCGGTTCCATACGGTACGCCACAAGGCAATTCATGACATGCCCTTCAAGTACCTCTGTCACTTTTTCTGCACCAGTCTGGGTTGATGCATGCCTAGGTGTTTTCTCTCTCCCCCACCACCACTATCCAAAAGATGCACAGCAGGGAAAAGGAAAAGAATCATATCATCATCCTCTTCCTCCCGCTTCCGACGTTTAGCCCTTGAATCCATTTTAATTCCAGGAACTAGACAAGCTGGTAGAAGATGACGACGAGGTCCTGGAGGTTCTTGTTGGGGACGAGGTCCTGGATGGTGGAGACCGAACGGAGAAGGCCACACCGTTGTTGAACTCCGGCAGATCTGACGAGAGGCGGCGTCGTTTCCGGCGAGAGGAGGAGGCCAAAGTGACGGCAGGCGCCGGCGCGAGTAGATGCGCGGCCCACCGCCGGCACGCGATGGGATGAGCAGCGGCGGCGCGGGCGTGGCCCACCGCGGCGCGCGTCTGGACGAGCAGCGGCGGCGCGGGCGCCGCTCCAGTCGAGAAGAGGCAG

Coding Potentia
Explanation CPC Score
noncoding -1.06875
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0130500.1 12 19068415 A T
Osa12LNT0130500.1 12 19068195 G A
Osa12LNT0130500.1 12 19068264 C A
Osa12LNT0130500.1 12 19068448 C T
Osa12LNT0130500.1 12 19068712 G A
Osa12LNT0130500.1 12 19068845 G A
Osa12LNT0130500.1 12 19068908 C T
Osa12LNT0130500.1 12 19069027 T A
Osa12LNT0130500.1 12 19069182 T C
Osa12LNT0130500.1 12 19069258 A G
Osa12LNT0130500.1 12 19069553 T C
Osa12LNT0130500.1 12 19069589 T A
Osa12LNT0130500.1 12 19069739 A G
Osa12LNT0130500.1 12 19070200 T C
Osa12LNT0130500.1 12 19070351 A G
Osa12LNT0130500.1 12 19070518 A G
Osa12LNT0130500.1 12 19070976 T C
Osa12LNT0130500.1 12 19071318 G A
Osa12LNT0130500.1 12 19071893 T A
Osa12LNT0130500.1 12 19072265 G A
Osa12LNT0130500.1 12 19072433 T C
Osa12LNT0130500.1 12 19072437 T C
Osa12LNT0130500.1 12 19072396 T C
Osa12LNT0130500.1 12 19068421 G C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0130500.1 osa-miR5801 Cleavage 4.5 13.578 1 24
Osa12LNT0130500.1 osa-miR5808 Cleavage 5.0 13.578 1 24
Osa12LNT0130500.1 osa-miR5814 Cleavage 4.5 22.277 1 24
Osa12LNT0130500.1 osa-miR6251 Cleavage 4.0 15.559 1 21
Osa12LNT0130500.1 osa-miR396a-3p Translation 4.5 21.767 1 20
Osa12LNT0130500.1 osa-miR396b-3p Translation 4.5 21.767 1 20
Osa12LNT0130500.1 osa-miR1855 Translation 4.5 15.719 1 21
Osa12LNT0130500.1 osa-miR1320-5p Cleavage 4.5 18.042 1 21
Osa12LNT0130500.1 osa-miR2099-3p Translation 4.5 14.579 1 20
Osa12LNT0130500.1 osa-miR5083 Translation 4.5 18.65 1 20
Osa12LNT0130500.1 osa-miR5156 Cleavage 4.5 18.45 1 24
Osa12LNT0130500.1 osa-miR5501 Translation 4.0 18.863 1 21
Osa12LNT0130500.1 osa-miR5501 Translation 5.0 15.798 1 21
Osa12LNT0130500.1 osa-miR2094-3p Cleavage 4.0 9.439 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0130500.1 12 nan Morphological trait Seed RG543 RG81
Osa12LNT0130500.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130500.1 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0130500.1 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG457
Osa12LNT0130500.1 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