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

>Osa12LNT0137100.1

GATCAACAGCTCATAATAATTCACAGTGTATGTCTATTTTCAAAACCATTTACAACGAAAAGGCCGGTCTAATGGCGTCCCTTCCCCCCAACCTACGCCCAGCCGACCTCTCCAATCTCCTTTGCTTTCTTCCTTCCATTGGACCATTCACGGTACAGGGGAAGTATAATCAAGAGTTCTCCAATAGATTGTAACTGGTACTAATTAAGCAGCAGTGGCAACTGGAGTGTCAGGATGGGCTCCCCATTCAGTCCATGATCCATCATATACAGGAACGTCGGTTTTGCCAAGGCGGTGGAGGCCCAGAGCTAATATACATGCTGTCACACCAGTACCACATGAGGACACCAGGGGTTGATCAAGCGATATACCTTCTTGTTCAAATCGTTTACGGAGCTCTTCTGGAGGTAATAGCTTTTGCGAACTGTCAAGCAACTGAGGGAAAGGAACACATTTGCTCCCAGGCACATGCCCACTTCTTATTCCTTTCCGTGGCTCTGGAACTGCACCATCAAATCTAGGCTTTCCTCGAGCATCTATAAGTTGATGTGTCTTGGCATCAATGTTCTCTTTTACCTGGTCAAGATTCCAAATAAGATGAGGCTGCAACTTTGCTTCAAATGTGGAGGGACCAACCAACTGCCCCTGATAAACTTTCTCAATTGCTTCACGAGCAGCACTGGCTTTTAAGATGGCATCACTAGAGGCACTTGATTCAACATCATACCCAGAAGCACGCCATTGGGGCAAACCACCATCCAACACCCAAACTTTATCATGTCCGAAAACACGAAACATCCACCAAACACGAGCAGCGCTAAATAGTCCCTTTCCATCATAAACTACTATCCCATCTTTGTTGTATATTCCAAGCGAAGATACAGCAGCAGAAAATGCCTTTTCAGATGGCAGCATGTGCGGCAACTGACTCAAAAGATAATACATTCAATGATATCAAGCATGCCGAAAAACAATTAATCAGCTCAACAATAACCAACACAAAGAAATCAAGAATGATGCCATGTTTTGCAATTCATATTCCTATCATAATAAGGGCATTATGTTGAATTGTTGATCTACTTAACCAAACAGGATTAAAAAAACATGTTAATTTATTAGTGTTACTTTTTTATCATGAAGATTGACAGTAGTAGATGAAAAATACAGTCAAGGAGAAAGGGAAAGAAAATTTAAGTGCCATTACACCAGCTAGTACAATATAAAAGCTTGACGTGATCTGAAAGAAATCAAACTTGAGTAACTTATTATCACTTTTTTTACACCAATCAGGGGATTGGGACAGACCACCAGATCACAACACACACAAATGTTATCAACCGTGTTGTGATCTGTCAGTCCCTGTTTTACTTCACCAGCTTCAACCTTTTACCTTCTGGTGTTGCCTAAAGCTATTTTTGTTGACCTGTATGAGTGGAACTTAAATGTATTGACATACTGAACTAAATGCTTTCGCTTCATGTATTTAAGGAATTGGGTTTACCAGCCCCTAAATTTGCATAGCACAAGCCCATATTCTGGCAATTTATAATGTTATATTAATAAAAAATAACATCAGAAAAGCAGGATGATGTGGCACATAAAGAAAGTTCATATGATTAGCTAGTAGTAAATGAAAAAACAAGCTAGTGAGTTGAACTTACGCTTGATGTTCTGTCTGATATTCCATCAACATCAAAGAATAGCGCCCCAGGAATATGAGCCACCTGGTACTCCTGAAGAGGATTCCTTTGTTCGGCAGGCATATACCAAGAGGCATCAAGTACCTTCACATCGGGGTCCTTGAGGTTGGCGTGCAGCCACTCGGCCGAAACCACGGGCTCCGTCCTCGGCAGCGCGTTGGTAGCCTCCGAAACGGCCGACGACGAGGTGGCGTTGCAGCGCGCCGCGATCCCGAACGAACCGACGCCCCCCAGCGCCGCCGGCACCGACGCCCTGCACCCGAACCCGGCGCCCTCCTCGGCGGCGCGCGCCCATCCGACTCTTCCCCCCGCGAGGAGCGAGGCGATGGTGGTGGCGAGGAGGATGAGGAGGGGAGGAGGAAGGAGGGTTTCCTTGGGGAGGGAGGAGGACAGTATGTGGTGCGAGCGGGCGCCGCGGAGGGAGACGGCGGCGGCGGCAGCGGCCCGGGAGAGGAGGGTGGCCGCCATGGATAGGGTTTTGGGGGGTTCTAGAAGGTTCGCGAAGGGGTTGGTGGCGGAAGCGAGAGGAAGAAGGGGAAGAGGTGGAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.973115
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0137100.1 12 25702164 G C
Osa12LNT0137100.1 12 25702373 A G
Osa12LNT0137100.1 12 25702477 G T
Osa12LNT0137100.1 12 25703483 T C
Osa12LNT0137100.1 12 25704131 T A
Osa12LNT0137100.1 12 25704267 T C
Osa12LNT0137100.1 12 25704531 C A
Osa12LNT0137100.1 12 25705668 T C
Osa12LNT0137100.1 12 25705739 C A
Osa12LNT0137100.1 12 25706660 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
Osa12LNT0137100.1 osa-miR5532 Cleavage 2.5 14.045 1 22
Osa12LNT0137100.1 osa-miR5532 Translation 4.5 17.159 1 22
Osa12LNT0137100.1 osa-miR414 Cleavage 5.0 24.803 1 21
Osa12LNT0137100.1 osa-miR815a Translation 3.5 8.145 1 21
Osa12LNT0137100.1 osa-miR2097-3p Cleavage 4.0 10.034 1 22
Osa12LNT0137100.1 osa-miR2099-3p Cleavage 5.0 18.972 1 20
Osa12LNT0137100.1 osa-miR2102-3p Cleavage 5.0 14.517 1 22
Osa12LNT0137100.1 osa-miR2105 Cleavage 4.5 16.262 1 20
Osa12LNT0137100.1 osa-miR815b Translation 3.5 8.145 1 21
Osa12LNT0137100.1 osa-miR815c Translation 3.5 8.145 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0137100.1 12 qLEI 4 Resistance or Tolerance Submergency tolerance RM5479 C901
Osa12LNT0137100.1 12 nan Resistance or Tolerance Submergency tolerance R1709 RM235
Osa12LNT0137100.1 12 nan Resistance or Tolerance Submergency tolerance RM5479 RM6953
Osa12LNT0137100.1 12 qSD12 Physiological trait Germination/dormancy RM3331 RM235
Osa12LNT0137100.1 12 qLEI12 Resistance or Tolerance Submergency tolerance nan nan
Osa12LNT0137100.1 12 qNEI12 Resistance or Tolerance Submergency tolerance nan nan
Osa12LNT0137100.1 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