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

>Osa01LNT0013200.1

CAATCAACAATCCCATCAGTCCATTTATTTCTGGCAAAATTGATCTTACATCACCCAACGATCCCGATTTTAGTTTTCTAGCACCGACAAATCCCAGGTCACTTGAATAGCATGGAACCAATTTCGCCTTTATTTATCGTATACATTTGTATGTCTGAAACGCATCCTCCGAAAGACTGCATCAGTGAATGTTAGTGAACCTCACAGTTTGGATGCGTTGGCAGTAGCAACCTTGCTTCCCAAAGCGATAGCTGCCTTGGACCCAGACTGGCGCCCCAGATGGTTGCAGATGAACTCGCCGGCGGCCATCACCTTGCCCAGGTCGACATTGGTGCTGATCCCCAGCCCGTTCAGCATGTACACCACGTCCTCCGTCGCCACATTGCCCGATGCACCTTTCGCGTATGGGCACCCTCCGAGGCCCGCTACGGAAGAGTCCACAACGCTCACACCCATCTGGAGAGAGATGAGGATATTTGAAAGCGATTGGCCGTAGGTATCGTGGAAATGGACAGCAAGCTTCTCCTTTGGAACAAAGAACATAACAGCCTCAAGCATTGGAACAACGGTGCCTGGGGTACCAACGCCTATTGTATCACCAAGTGAAACCTCGTAGCAGCCCATGTCATAAAGCTCTTTAGCCACATGAGCTACATTTGACGGTGGCACATATCCTTCTACTGGGCATCCAACCACACAAGAAACATACCCTCGCATGGGGATTTTTAGCTCTTTTGCTGCAAGAGCAACATCTTTATAGCGAGCAAGGCTCTCTTTAATGGTACAGTTTATGTTTGACTTGGAAAATGCTTCAGAAGCTGACGCAAATACTGCAACTTCTTTTGCACCTGCTGCAACAGCTGCCTCAAATCCCTTAAGGTTTGGTGTCAATACAGGAAGGCTTACACCTTCAATATTCCGGACTACATCCATCACATCCTTAGCATCAGCTAGCTGTGGTACCCATTTTGGAGAGACAAAACTAGTTGCCTCAACAACCGATAATCCAGAGGTTGCCAGTCTCTGTATGAGTTCAATCTTTACATGTGTTGGAACTATGTTCTTCTCATTCTGTAGCCCATCTCGTGGCCCAACTTCCACAATTTTCACACTTCTTGGAAGGTCATGTATAATCTTGTTACCAATTCCTATACTCTGTTGGCCAGAAGAAGATGAAAAATATCTGTAGTTCTGCGGATTCAGTGAAGCACCATTTGCATATGTAAAATGACGTTTCTCCCCCAAAAATAACTTGAACCGATGCGGCATTAGCTGTCTTTGGTATATCTGTCTTGTGCAAGGATTCTCTTCCCTACCGCAAACACGAAATTTAGCTCAAGCCAACAGATTACAAAAGAATAGGGCAATTTTGAATCTACAATTTCATTATCATTTTTTGGGGCAAACATTTTACTAAAGATTTACTAAATGCGTAAACCTATTCAGTGATCCAGATAAGGTGCAAGCGCTTGAGCACAAGAGAATCAGAAGATTCAGAACGCCGAGGCAGACTCACGCGGGATTGTCCGACGAAGAAGAGCACGGCAGCGGCAGCGGTCGCGGCGCACCGGCCGCGCCACACCCAGTCTCGGCGAGCCCGAGCCCCGCACCGGGCCGCGCGTCGCCGCCACTGGGGTGACCCGGCGACCTTTCTTGGGCCGGCATCCCAGAGCTCGGCAGTAGGTACCTCGCCGCCGCCGCCGCCGATGAAGAAGAAGAAAGGGCGCGCGGCGAGGCGGGGGAAGACGGCGACGCGAGCCTCGACCAGAGCTTTGACGCCAGCATAACCACGGTAGGGGGTCAGCGCGGCATCCCCCGACCGGAGGGAGAAGCTTCTAGAAGGTTCCGCGCGTCGGAGGAAGGAGACGAGACGAGGCGAGAAGCGAGACTGATCGGTTGCGTCTGGACACTGCGCGCTTCTCTTCTCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.960923
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0013200.1 1 9272434 A G
Osa01LNT0013200.1 1 9272589 A G
Osa01LNT0013200.1 1 9269062 T C
Osa01LNT0013200.1 1 9269122 G A
Osa01LNT0013200.1 1 9269948 T C
Osa01LNT0013200.1 1 9270162 G A
Osa01LNT0013200.1 1 9270841 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0013200.1 osa-miR530-3p Cleavage 3.0 16.238 1 21
Osa01LNT0013200.1 osa-miR5074 Cleavage 5.0 21.655 1 21
Osa01LNT0013200.1 osa-miR5498 Translation 4.5 17.164 1 21
Osa01LNT0013200.1 osa-miR5500 Translation 4.0 18.169 1 22
Osa01LNT0013200.1 osa-miR5536 Cleavage 3.5 12.967 1 22
Osa01LNT0013200.1 osa-miR169i-5p.2 Cleavage 5.0 12.716 1 22
Osa01LNT0013200.1 osa-miR5074 Translation 5.0 9.308 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0013200.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0013200.1 1 An9 Morphological trait Panicle/flower nan nan
Osa01LNT0013200.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0013200.1 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0013200.1 1 nan Resistance or Tolerance Insect resistance RM576 RM3412
Osa01LNT0013200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0013200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0013200.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
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