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

>Osa09LNT0435500.1

ATGTGGAACTGTGGAAGATAGTAACCTTGTTGTGCTTTCTGCAGATATCATCCAGTCCAATTAAAGTGAACAATTCCACCCTTAGTCTCTCTTCTGTTGGACAGGCACGGCCAGGCCATAGAACAGCAGCACCAGCATCAGGAGGTAGCCGACGACGACGAGGGCGACCAGCCTCGCGTCATCTCTAGCCAGATATGCAGAGAAAGCCGAGTGGAGGGTGAGCACGGCGAAGGCCGTCAGCCGCAGCCATGGCGATCCATCGCCATCGGCTGCGGCAGAGGAAGAAGAAGAAGAAGCAGAGGCTCTTCTGGTAGAGTTGTTCTTGCCTTTCTTGGCCATGAAGAACAGCAGCTTGAAGGGGATCCCTTTTCTCTGGGCTCTGGACAAGGTGAAGGCTGATGCTTTGCTTTGCTACGAAGCTTCCCTGAGTGAGTGGTAGACTGGTAGCTTTCACTGCTTGTTTGCCACCACATCAGAGAGGATCAGGCCTATGTGACAAACAATAAGCTTTGTTGAATGAATCCATCATAATAGACAACAAAGTCAAGGCATCTGATTCGGACAACACAAGAGCCTCCAAGACTGCAAGTCACTGTCACGCTACCAGAACTATGCTCAAAGGACTTTGGAAGATGGCATATAGGAGGTATTGAAAATTTGCATCGATGCAGCACAAAATTGGTGGGTTGGAGAATATTTTTTAAGTTTACATATAGCTGAAGCTGTTCTCCCAGATTCAGGAAGAGAAACTGCTGCAAATTTCAGGGTACATCAAAGTTGTAGGTTTGAGTTCAATATGATCTTGGAAAAGCTTACATCTCAGCTGCTGAACTGCAGCGCGATGCAACAGCATGAACATGCATCTAATATGTAAAATACAAACACCTTTTTCGTTCATCTATGAGGGTCTCCTAATCCAGGTTGAGTCAAGCGAAACTTGATCATATGTGGTTAGCCCTAGGTTGTCACTTCGTCGAGGTGCCACCTTTTCGAGAAGAAGAATCAGCATCAAACTGGGCATAGTAGGCAGATGTTTCTGATTCCAATAGGATTTGCCTGAGATTCTTGTCTTCCAGATGTTCCTGCAAGTAATAAAAACATGGAACATCCATAGATTCGTTTAGCGAAAAACAAGCATCATATTCATAGGAGGAACATAATTTACCCAGAGGCCTGTCACAAGTGAAACAATGGTGATGGGAGGCATGATTTATGTTAAATTGAAGAAATCCTGGGAAATACTCAGACAAATATGTTATGATGAATACCACAACATGATCACTCTTTTGTCAGATTTCAGAAAATTGATGCGCTCAATCCCCAAAACATGAATATTCACGTTATTCTGATAACTTAGTACTATAAGAAACAAAACTCATCAAGAACATTGAATTTTGCTACAAATGGGCTATCTTCAGGCTGGGTTGCCAACCTCCAACACACTGGGCTAGCCCTAGTGCAAATTCTCAGTCAGCAATACACTAACTACAATTGGCTAGAAGCTGATACAATGGTGCGAATTCACCATGTAGGAAAATGGTTTGGAAAGCATTCAGATGCCAGTTAGCAATACAACAATACCAGAATATTCTTCCCCAACTGTTTTCCATAAACCAATAAACCAAATGCAAGGACAACTACACCGTTGTGTAACTTCTGTTCAAGAATGGAAAATAGATGCCTGTATTGCTAGTTTCAGAAAGGTTTCTGAATTTCTAATTGCACACAGCAGCACAAAATTTTTTTCTTAAGACAGGCCAGCCCAAAGATTGACCTGATGAATTTCATCAAGATTTATGAGATCAAATAACAAAGAGACAGTATAGACAATCTACAAAAGGGCTGTCAAGTGACGGAAAGGCGATTCCCTCAAAACTCTATTGCAGCCACTATGCTGCCATATAGTACAACTCCACTCTGAATGTCTGAATGTCAAAGAGCCCCACTTCTCACCCAAACAGTTGCATAGTCGATTTGGACTAAATCCCTAAAGATCCGTGTGTGTTTCCATACTTCAAGTGCGAAAAAAATGAACAATCAGCACCAGCGAATCAAGCAGCACTAATCTCACACATTTGTAACGGAGGAATTCAACAGGCCAGCGCAGCGCATGCGCCGCCTAGCCTGAATCATGACCAACAAACAGACAGAGGTCTAACTAGGAGCTCCAAATCAGATGATTCTTCAAAGAAGAATCCCCTTTAGGCTTTAGCCATCACCATTACATAAGCCACTTTATCAACTTGATCTAGCAACCAACACACTAGAAAACAACTCGATTTCTTGCCATATAAACTAAAAACCTACTTAAATGAAACCCCATCCTAAACTGCGAAAACACAAGAGCAATCCCTAGGGCAGTCGTCTTTGCAACAAATTGAGGGGATCGGTAATAAATCAGTGATGCTGTGATCGAATTCGGAGGCGGCGAGAAGGGAGTGACCTCGAGGCAGGCGCGGTACTTGTGCCACTCGCCGACGCAGTCGTCCTTGTGCCATTGCCCCTTGGCGAACTTCTCCGCGTACCAGCGGTTGAAGCACTCGTGGTACGCCGCACGCAGCTCCGAGCACGCCGCCGCGGCCGCCGAGGAAGCCGCCGCAGCAGGGGGAGGAGACGCCGTCGACGAGGACGACTTGCTCCGGCCAAACACCATCCTCTCAGGCTTCGGCTCCCTCGCCGCCGCCGCCGCCGCCCGCCGCCGTCTGTCTCTCTCTCGTTCAGAAACCCCTGAAGGCGGAAATCAAGCTTTAC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.72069
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0435500.1 9 11813843 C T
Osa09LNT0435500.1 9 11815327 A G
Osa09LNT0435500.1 9 11813448 C T
Osa09LNT0435500.1 9 11813862 A T
Osa09LNT0435500.1 9 11814078 G T
Osa09LNT0435500.1 9 11814501 T C
Osa09LNT0435500.1 9 11814534 G A
Osa09LNT0435500.1 9 11814807 T G
Osa09LNT0435500.1 9 11815028 C T
Osa09LNT0435500.1 9 11815844 A G
Osa09LNT0435500.1 9 11816580 A C
Osa09LNT0435500.1 9 11816668 T C
Osa09LNT0435500.1 9 11816831 T C
Osa09LNT0435500.1 9 11818038 C T
Osa09LNT0435500.1 9 11818233 C T
Osa09LNT0435500.1 9 11818310 G C
Osa09LNT0435500.1 9 11818426 G A
Osa09LNT0435500.1 9 11818583 G T
Osa09LNT0435500.1 9 11819443 G A
Osa09LNT0435500.1 9 11819988 A T
Osa09LNT0435500.1 9 11820089 C T
Osa09LNT0435500.1 9 11820414 A T
Osa09LNT0435500.1 9 11821006 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa09LNT0435500.1 DTM_#DNAt_MULE_japo_Os3366 Chr9 - 11815941 11816451 510
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0435500.1 osa-miR6256 Translation 5.0 9.886 1 22
Osa09LNT0435500.1 osa-miR166g-5p Translation 5.0 18.343 1 21
Osa09LNT0435500.1 osa-miR2055 Cleavage 5.0 15.535 1 21
Osa09LNT0435500.1 osa-miR2871a-3p Cleavage 5.0 7.169 1 21
Osa09LNT0435500.1 osa-miR2871b Cleavage 5.0 7.169 1 21
Osa09LNT0435500.1 osa-miR171i-3p Translation 3.5 12.416 1 21
Osa09LNT0435500.1 osa-miR1882a Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882b Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882c Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882d Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882e-5p Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882h Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882f Cleavage 5.0 24.07 1 24
Osa09LNT0435500.1 osa-miR1882g Cleavage 5.0 24.07 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0435500.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0435500.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0435500.1 9 qLG-9 Physiological trait Germination/dormancy G103 R1751
Osa09LNT0435500.1 9 nan Resistance or Tolerance Drought tolerance R1164 R79
Osa09LNT0435500.1 9 nan Morphological trait Shoot/Seedling RG553 RZ206
Osa09LNT0435500.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
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