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

>Osa01LNT0021000.2

ACCAGCAGCAGCAGCCGCCCAGTTTGAGCAGCAGCAGGAGTTCAGTTTCATAGCAGCAGCAGCGGTTCACTTTCATTTCAGCAACAGCAGCAGCAGCACAATTTCCAACAATAGCAGTATCATTCCAGAATCAACGACAGCATCATTCTAGCCAACAGCACCATTAAAGCATCACACAACCATCACCAAAATGAAGTCACCATTCTAGTTGCAGATCATTTATTCCTAATATTTAAAAAGGCCACTAAATTTATTTGTTCATTACACTCCTTTAATAATAAATAATCAGCAATGAACTGCAGCCTTGCAACGCAATCAACAAAACTGTGTGCTTCCGTCGGAATCATCTCAGGGCAGCCAGGTGCGCCACAGTTATGCTGCCCAGGGACGTCGCCCCAACGTTGAACTGCAGGAGGAGCTACTGACCACCAGACAGGGTAAACCACAACTCCATGATCTTCATCCAGGACCTAATTTCAGAAACCAAGCAGCAACCAGTCAAGTTAGGACACAGGAGGCAGCTCAATTCTGTAATTTTCTGAAATTGGAATAAATCAAGTTCAATTCTGTAATGTTTCTGTCAAAGAATTGTTTTATAGTTCTAAAGCATTTCAGCTTATTTGCCTCTGTACACATGTAAAATAAATTAAGTGCCTCAGTAAAGCACCAACTTCTGAATGTTAAGAGTTTGTTTGAGATAAGTTGAAAAAGGAATGGCCTATCTATTGTACCTAAAACATCTATCAGCCACAGTCGTAAATAAACCACCAATCTGTCATAAGCATAAAACTTGAACAACTACATGAACAGATTCAGAGACAATGTTGGAAATACACAGAAGCACAGCCCTCCCCTGTCGTGCAACACATTCTATTCCATAACTGTGTTTCACTAGTTGTGTTCCAGTAATCAACATAATAAAGTGCAAAAATTAAAAAGTCACATTAATGTTGGAAGAAAAGGTTTAGTGTGAAGCCCTCTTATTTGCGTAGGACTCACGGCACGGCTTCAATCTCTTAGAAGGAATCCTTCCTTTAGGAACAATCTTATGTGGATCGAGGACTCTCTCACCACTGGGTTGGTTCGACGCTGAGAAGTGCGCCGGCAAAGGACCAAGTGTTGTCTCATTAACGCTACCCTCGTTCTCGGCACCTTCCCGCATAAAATTTTCAAAGAAATCAATGACTTGCTGTGACCTCTCAAAACTCAAAGAAGCTTTGACTAAAGCCTCATTAGCTATGTTACGGAGAAGGCGGTACTGATCCATCTGTTCGGACCACTCATGCACATTTGCAGTTCTAATTGAAGGGAACGCTGCCTTCGCTTGCAATGTCCATCTAACCGCAACACAGCACTGAGGAATAATGTCAATTCGGAGATACTTCAGAACTGTAAATATATGTGAGCATGGTATCTCTTTGCTATCCATCATCTGACAGTAACACTTCACGCCCATCAACAATGCACCATCAAAACTACAACTCACTTCACCATGCACTTTATGGTCATATTTCGAAGCAATACTGTACCTTCGAGCCTCATCCAGTTGCCTCACCTCCAAAATCACCCATTTACAAATCTTCCGAATCTCTGCCCTTACCTCCCTGAAAATGACATGGGTGAAAAAGCGTGCAGCACTAATTTTAGTGAATGGTACCGATTGTGATGCTCTAGCATCCATCTCAGCCTCATTTCTACGCATACGCGACACACAGCACATGAAATGCTCTATGACATCGATCAGTGACATTTTCCTGTCGAGATGACTATGAATTCTTGAGTTCAAACCCTCACTCCTTTGATTGCTCCTCATCCCTAAGAAATATCTCCCATCGGTATACGCCGCGGCCCACTTTTCCCTTAGCGCATACATCATGGCTAGCCATAACTCCTTCTCCGGCACATTATCCCTGTTCTTAAAGGCACACCATCGTCTCTCAAATTCATCGGCCTTCATTACTTCGTAGACGAGTCTACGAAATTTGGTGAGCGCATCCCCATGGAGATGGCGTTTTGCGTTCTCCTCAATGTACCATGTACATAACCGATGATCTGCATCAGGACAGACCTTGGCGATGGCGTTTGCCATGGAAAGGTCCCCATCGGTGATAAACGATCTAGGATGCTTGCCACCCATCGCCTTAATGAAGGTCTCCAGCAGCCACACATATGAAGAAACCGTCTCATCTGAGAGCAGACAACACCCAAAGACAACCGTGCTACGGTGATGGTTTACACCAATAAAAGGAACAAAAGGAAGGTTGTACCGGTTGACACGGTAAGTGGCGTCAAAAACCACAACACCTCCAAATGCGTCATAGTTGATCCGAGATTGTGCATCGGCCTAGAACATATTCTTCAGATGACCTCCGGCATCAGTATTGTACTCAAAGAAAAATTCTGCATCTCTTTCCTTCTGTTCGTTCAAAAGGCTCAGTGCAAATTGAGTGTCCATACCCTCAATTCTTTCTTTCTTGTAACGAGCAACGAAGTTGTACAAGTCCCGAGACACAAACCCAACCTGATCATAACCACCATGATTCTTCTCCATGACGTCCATTATATTGCATGTACGAAGGCCACTGACCCCGAGTTCTACAACCTCAGCCTTTTGAGCATCACTTAGATTCCGATGGGATCATAAGAATGCCACTTGGTCATGCTTTGCAAGTGGGTGCGCATGACCATCGTTGAAATCTTTAACAAACCAAATCCCCATCTCCTCATTCAACTGTATCTCAAGTTTGGCCTCACATCCGCAACGTGTCAGGGCCCTTGGCTCCCTAATTTGGTCTGTTCTTTCAAAGTATTTCAACAACCTATAGCCTTCATATGAGCAGCACAAACGCCTCCAGACCACCTTACCATCTCCATTGTACCTAACATTGTCCTTTCTGATGCTAAAACCTTTCGACCAAGCATAATCATTATAGAACTTATATCCTTCATCCTCGCTTCTAAACTCCTTGGTTATCACACTCTCATACTCTGTGATCTCCTCCAAACTAATGTGATTGCCAGCCATGCCAAAATTTAGGGCCAAGAGAAAAGTAAAGTGAGGGGCGCCGTGGAGCGCGGGGGCGCAGGGGTGGCGCGGCGGCTCGAAAGGGGAGGGTCGCCGCGGGAGTGAGGGTGCAGGCGCGGCGCGGCGCCGCGAAAGGGGAGGGTCAACGCAGGCGCGGCGGCGCCAAAGGGGAGGGGCGCCGCGTCCGCGCGAGGGTGGAGGGGCGGCGCGGCGGCGTGAAAGGGGAGGAACGCCGCCTCCGCGAGAGGGTGGAGAGGTAGTGCGGCGGCGTGAAAGGTGAGGGACGCCGTGGCCGCGCGAGGGTGGCGGGGCGGAGCGGCGGCGTGAAAGGGGAGGAGCGCCACGGGCCGCGCGAAGGTGGCGGGGCGGGGCGGCGCAGCGGGGGGACGGAGAAGATGGAGGCCATAAACCCCCC

Coding Potentia
Explanation CPC Score
noncoding -1.09173
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0021000.2 1 18461664 T C
Osa01LNT0021000.2 1 18459298 C A
Osa01LNT0021000.2 1 18460421 G A
Osa01LNT0021000.2 1 18460478 T C
Osa01LNT0021000.2 1 18461608 C T
Osa01LNT0021000.2 1 18462052 A T
Osa01LNT0021000.2 1 18462074 T C
Osa01LNT0021000.2 1 18462087 C T
Osa01LNT0021000.2 1 18462436 T C
Osa01LNT0021000.2 1 18462857 C T
Osa01LNT0021000.2 1 18463359 C T
Osa01LNT0021000.2 1 18463500 G A
Osa01LNT0021000.2 1 18462702 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
Osa01LNT0021000.2 osa-miR5797 Cleavage 5.0 17.462 1 21
Osa01LNT0021000.2 osa-miR397a Cleavage 4.5 12.063 1 21
Osa01LNT0021000.2 osa-miR397b Cleavage 5.0 12.063 1 21
Osa01LNT0021000.2 osa-miR171f-5p Cleavage 5.0 13.084 1 21
Osa01LNT0021000.2 osa-miR1426 Translation 5.0 16.63 1 21
Osa01LNT0021000.2 osa-miR1856 Translation 4.0 9.511 1 21
Osa01LNT0021000.2 osa-miR2096-3p Translation 4.5 20.817 1 21
Osa01LNT0021000.2 osa-miR2864.2 Translation 4.0 14.908 1 21
Osa01LNT0021000.2 osa-miR1862f Cleavage 5.0 10.441 1 20
Osa01LNT0021000.2 osa-miR1862g Cleavage 5.0 10.441 1 20
Osa01LNT0021000.2 osa-miR2873b Cleavage 4.5 9.979 1 21
Osa01LNT0021000.2 osa-miR2873b Cleavage 4.0 13.888 1 21
Osa01LNT0021000.2 osa-miR2873b Cleavage 5.0 10.67 1 21
Osa01LNT0021000.2 osa-miR5797 Cleavage 5.0 12.204 1 21
Osa01LNT0021000.2 osa-miR5808 Cleavage 5.0 20.405 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0021000.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0021000.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0021000.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0021000.2 1 nan Morphological trait Root RM23 RM306
Osa01LNT0021000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0021000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0021000.2 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0021000.2 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
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