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

>Osa02LNT0172400.2

TTAAAGTCTACAAAAATATCGCATTGATTCCCCTTCACCATGAGATGCAACTGGGTTCCATCTTGGCAGGAGACATCGGATGATCGCCATTTCTTTTATAGAACCTCCAAAACTGCAGGCAAAACTAATACAACTTCAAGAGTACTGTATAGAAGAGGCTAACAGTCAACTGATTGTATGTGATCTTCAGTTTCATCCTTGAGACATTCGCTAGGTAGCTGAAAACTTAAACAGAACATAGCCTGCAAGAAATATAAAACACAATATATTAGGTGTCACAAGAACTAGCAACAAACATAAAAAAATATCCATTGCTTAGTTACTTTCCCAGATTATGCAGGAAAACTAGAAAAACTATTATTGGTGGCTAACCACAAAGTTCTTAAAGACCATTCACCAAGAGACAGTTTCTGCTAGGAAAATATTATGGGCGGTGGGCCATACATTGTGCTCTCAAACAAATGAAAAAGATTTCTGTATCCTAAGATCAACAAAATAAAGAAATTTGTGCATGTAATCTTGCAGACAATAAACATGAATCTTAGTCTTATTATATGAGACAGAGGATACCTTGTTAGGTGCAACATCACGAACCCTATGGAATATGGGCTCTGCTATCTTCGCATTCAATTTATTTTGTGCTTCGGATAATATCAATTCTTCAGATTCACTTGAACGGATGAAACAATAACAGTGGATCCAAGGTAATGGTCCGGTCCAGTATTTCTTTTGGACAAGACCACTGAAACAATCAAGAAACTGCAGAGCAGAAGCAGGTAAATTCATTACGACATGGTCAAAGTGTTCCCATGGCTTGACAGGTGGTGGTCCTGAGCCTTTTACTCTTTTGTTGTTCCTCTTCTTTGTATGACTAGCATCTTCTTGGCAGTACCCATCACCTCCATTTGAGCTTTCTTGACGCCTTTTTGTCGCAGTGCTTATCATGGATGAGTCATTTATATCCTTATGGCAGCTCTCTTGAACATCACTATGATTTCCATTTGAAGTCGAACTTTCATTAGCAGGGTCAATGTCTTCACTAGAACAATTAGCAGCAACTTGAGAGTCTGACTTATTTTCTGAACAAGGCACTTCCAATAAATTTTGCATGAACACTCTGGCATCCATGTTATATGTAAATATATAATCGTCCACCTTGTTAATCTGTGCATTTGTTCTTAGATAACGAACACTGTCTGGATTTAAATCATTTGCATATACAATACATCCTTTCTGTGCAGCTGGAATCGAAAATGGGCCAATACCAGCAAACATGTCACATATAACATCTCCTTTCTTGAAAAGGGAAACCAATCTGATGTGTTCATGCTCAAGCCTCGAATTCCAGTAGACTAATCCATAATCAAGTTTAAATGTAGCGCCATATTGTTTTACTTCAGTTACCATATCGTTTTTCCCTGCTAAGATTTCAAACTGCGGAACTCGAAACTCGTTTGTAATGGTCCCAACTTTATTTACCACAGTCTGAATCCTTGGATAATTTTTATCATAGATGACCTTTGCTATGACATCTTTGTATGGAAGCAAGTCATCAGGTATGTTCAGATGTGCAACATGGCCAATTGTTTCAAAAGAAGAGGGTACCTCCACTCCAGCAGGCAAGATCTGCTTCAGAATATGATCTGCACTCCAGTAAGAATAACCAAGGGTCAAACTGTAAGGTACAACATCAATGTTGCAAATTTGCTTCAGTGAATCGTAAACCTTCTCCTCAATATCAGACAGGTCGGGGTTCTGGATCTTCTCCGACAACACGACGAGCCGGTTCTTGTCGCTCTCGGGATCCTCCACGACTGGCTTCACCCGCGGCTTGTCCAGTAGGTACCCGGAGCGGAGCAGGCGGGTGACGGCGGAGGCGAGCTCGCGGGGGATGCGGAGCGCCCAGAGCTGCAGCCGCTGCTCGAACTTGCTCTCGTCAAGCTTCTCCATGGTGGACTCTGACTCTCCCCTCCCTTCGCTGCTCTCCTCCTTGCCTAGGGTTTTGGCGCCGCCGGGGAGGTGGACGCACGTGGCGGCCGGAGTCCC

Coding Potentia
Explanation CPC Score
noncoding -1.2837
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0172400.2 2 23762070 T C
Osa02LNT0172400.2 2 23761026 A T
Osa02LNT0172400.2 2 23761260 T A
Osa02LNT0172400.2 2 23761494 T A
Osa02LNT0172400.2 2 23761506 A T
Osa02LNT0172400.2 2 23761678 T C
Osa02LNT0172400.2 2 23762212 T C
Osa02LNT0172400.2 2 23762956 G T
Osa02LNT0172400.2 2 23763021 G A
Osa02LNT0172400.2 2 23763158 C T
Osa02LNT0172400.2 2 23763497 C A
Osa02LNT0172400.2 2 23764425 A C
Osa02LNT0172400.2 2 23764873 C A
Osa02LNT0172400.2 2 23765187 A G
Osa02LNT0172400.2 2 23762046 G A
Osa02LNT0172400.2 2 23764260 T 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
Osa02LNT0172400.2 osa-miR2104 Cleavage 4.0 20.334 1 22
Osa02LNT0172400.2 osa-miR2105 Translation 4.5 15.037 1 20
Osa02LNT0172400.2 osa-miR2868 Translation 4.5 20.056 1 20
Osa02LNT0172400.2 osa-miR2878-5p Cleavage 4.0 12.056 1 24
Osa02LNT0172400.2 osa-miR5519 Cleavage 5.0 23.749 1 21
Osa02LNT0172400.2 osa-miR1847.1 Translation 4.0 13.362 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0172400.2 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0172400.2 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0172400.2 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0172400.2 2 qSB-2 Resistance or Tolerance Sheath blight resistance G45 RZ273
Osa02LNT0172400.2 2 nan Physiological trait Eating quality C621 C370
Osa02LNT0172400.2 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0172400.2 2 qRPA-2-c Resistance or Tolerance Other soil stress tolerance C424 G45
Osa02LNT0172400.2 2 Tiller number Morphological trait Culm/leaf R26 C424
Osa02LNT0172400.2 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172400.2 2 nan Others Others C424 G45
Osa02LNT0172400.2 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0172400.2 2 qGRH-2 Resistance or Tolerance Insect resistance C621 C601
Osa02LNT0172400.2 2 qPN2 Morphological trait Culm/leaf RZ961 RZ401
Osa02LNT0172400.2 2 Sn2a Morphological trait Dwarf C424 G45
Osa02LNT0172400.2 2 qPTD-2 Morphological trait Panicle/flower C424 G45
Osa02LNT0172400.2 2 qPH-2 Morphological trait Dwarf RG324 RG83
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