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

>Osa12LNT0126800.2

GATGACTCCGCCGCCGCGCTACTTGCTCCGTGCCTCCTCCCTCTTTCCCCGACGGAGATGAGGTAGTTCCCCACCGCCACCGCACTCCACCGCGGCCTGCCCTCGCCGGCGCTGCTCACCCTCGCGTCGATGGATCCGACGCCCTACGCCCACCGCCCTCCAGCCATCCGCTGCCGTCTGGCGTCTATCGCCGTCAGTATTGGATGCAGGCCGCTGCCCCGGCGTCGACTGCTCTCACTATTGGATCAAGGCCGTCAACCACCGTCGGGCGTCATCCACTGCCACGGCCGCCCGCCGCCCAATCGAGCAGGCCAACACCCCATCTCCAACGCCTGCGAGCCTTGTAGGTGAACCATGTACAGAGGATGCTGGTGGAGGTGTGGGGGCTAATCACTAATCAAACATATTTTCGTGGATCTAACTTATTACCTGAGTTCTCCTCTTTGGTGATGGAGCCGGTTCAGGTGCCCTGTATGCCTGTAATGGAATAGTTGCCACATCCCCAGGAAATCAAGTAATTTAAATACTTCTCTATTGAATAAACTACATAAACGACATAACGGTGATTCAGTAGTTTTTATCATTATAGTTGTTATCGTTGTTTTTTTGCTGGTGACGGTGCTCTTATACTGATAATGCATAATGAATCACTGTGCCATGAGTAAAATCTGTTTTATTGTAGAAGGAGTAAAAACTGTTCACTTGTTGCGTTAATGTGTCCCTGACTCCCTGACATGTCAAGGAGACTGACAAAAGGATTTGAAATATTCCAATCGATGTGGTACTTCTTCACTAATTCGTTATCAGAATGGTTCCAATGATGCAGCATAGGAGGAGGAAGAAGGTTCAAAATTCAAGCACAATGGAAGTCGGCAAGCACACATGTGGATTCAGATATGCAGTGAATAAACAAAGAAACAGTCTATTTCTGCCATAAAAGATTTTTTTGGACATGATATTTCTGCCATTAAAGATTGGCAATTGAACGAACGAATGTGCATGGTCTGTTGCATACACTGGTCGTTGTAGATGCTGAATGCATCGTCGAATTAAGCTAGGAATGTGATTGAGGGGCCGATGATGATTATGGTGTTTGTCACGAGTAACATTGACCTGATGGTGCCGGCGTTCAACACAACGGGTGACTAGTTGAATGGTCAAGCGGCTGCTTACGCTGGTGCCTAGGTTGGTAGACCTGGCGTGCTCAAGATCACCAGCGCGGTGAGCATCTCTGCCACCGATGCTAGGTGGTTGCTGAGGTGATGTTCTTCAACAGTGGGATCCCATTGCTGCTCATTGTCGAATGGGATGGCAAGCCAGTTGGTGATGGTACCTAAACTAAGTTTTGATTAATTGGAGCAGTGCTGATTGGAAAGAGAATATTATTGGAGCAATATTATTGGGAAAATGTATTTTGTGGGAGCAGTTTGGCAAGGGTTTTATTGGAGCAATTCTGGTTGGAATTATATTTGTATCGGATCAATACTGATTGGAAAGGATTTTATCAGACCAATGTTGATTAGGAAGGCATTCCCATGAGTTGCAAATCCAAGGAAGTTGATAACACCCATAGTCTCATACAATGGAAAGTTAACCTTTCTGCAATATTTCAGTTTGTCTCAACTTTCAATTAGCACAAACCGCTGCAGAGGCCAAAGCAACAAAAGCCATTTTGGCACAGTTGCAGTGCCTAGAAAACATCAGAAATTGAGAAGAATATATACTTTGTGTGGTGAATGTGAGCTTGAAGTGCAAGAAGGTAGATGAGCAGTTAGACCTTTCTCAGAAGTAAAGCGTCTTCAAGCACAACTTCTGGCTTTTGGGAGTCTCTGAGATCGACATGTTCCTAGCTAATCGATTTATCAACTTCAATATCATCATTTAGTAAACTTATAGTACTTTGTTAACATGGAATTAGGTGTGTGACTTCTAAAGTTATATAAAGTATCATCAAGAGTAAAGTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.321556
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0126800.2 12 13488916 T C
Osa12LNT0126800.2 12 13487365 T C
Osa12LNT0126800.2 12 13487394 A G
Osa12LNT0126800.2 12 13487525 A G
Osa12LNT0126800.2 12 13487533 A G
Osa12LNT0126800.2 12 13487613 G A
Osa12LNT0126800.2 12 13487648 T C
Osa12LNT0126800.2 12 13487773 A G
Osa12LNT0126800.2 12 13488162 A C
Osa12LNT0126800.2 12 13488805 C T
Osa12LNT0126800.2 12 13489493 T G
Osa12LNT0126800.2 12 13489848 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa12LNT0126800.2 DTM_#DNAt_MULE_japo_Os0089 Chr12 + 13490723 13491466 10
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0126800.2 osa-miR5534a Cleavage 4.0 24.948 1 21
Osa12LNT0126800.2 osa-miR5534b Cleavage 4.0 24.948 1 21
Osa12LNT0126800.2 osa-miR1440b Translation 4.5 7.333 1 21
Osa12LNT0126800.2 osa-miR6250 Translation 5.0 13.017 1 22
Osa12LNT0126800.2 osa-miR166h-5p Cleavage 4.5 22.679 1 21
Osa12LNT0126800.2 osa-miR414 Cleavage 5.0 16.134 1 21
Osa12LNT0126800.2 osa-miR5148a Cleavage 4.5 13.714 1 24
Osa12LNT0126800.2 osa-miR5148b Cleavage 4.5 13.714 1 24
Osa12LNT0126800.2 osa-miR5148c Cleavage 4.5 13.714 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0126800.2 12 nan Physiological trait Eating quality RM247 RM179
Osa12LNT0126800.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126800.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126800.2 12 qtl12.1 Resistance or Tolerance Drought tolerance RM7195 RM28166
Osa12LNT0126800.2 12 qDLA-12-3 Resistance or Tolerance Blast resistance RG463 RZ816
Osa12LNT0126800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126800.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0126800.2 12 nan Morphological trait Seed RG543 RG81
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