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

>Osa05LNT0320900.2

ACTCAGAAAACTCATTCATTCAGTGATGCACTTCCCAAAGAGTCCTAACATGCCGGAAGCCATACAAAAGGCTTTTGCTACATGCTACTAGTAAACAACTTGCTGCTATACCTTTATTCAGTGCAAGCTATTATCAATAGAAAACACTGGCTTATCTAGACGCCTAGAATATTTTTTTAGATAAAGGAGATTTCTTGGGAATTATCCTGGTCACAAGACAACTTCCTAAGTTCTCGTCAGATACTTGCAGCATAAACATACTAGCAAAAGGCTAAACGACCAGCATGACACTTGGTACAACTACTCCAAGTATCTCGCAATGTGACTTGGCAGCTCAGCGCTGTTCCCTTCCATAGTCAGGAGCTTGTAGAAAAGATCCCTGCGCAAGGCAGCAACCCTACCCGAATCTAGAACATTGCTCAGCTTGCCATCATAGAACTCGCGCGCATAGTATAATGTGTGAAAAACAGAGTTCCATTTTTGGCACCTCGGGCTAATCTTTGTGTGGTACGTACATGTCCATCCATCCGGGTTAATATCCCAGTCATCGAAGAATTTGTTTATACATGTTAGCAAGCCTGTGTGGATCATCGTAACTGTCTGACGGTGCTTAGCACTCACATCGGAGACCTCCCGGTGTTGCAAGACAGGGTCCAAAATGTGCATTTGCCTCTTCTCCCATGTCCCAAATGTAGCATGCCCATGTATCACTAGCTAATTGAACCGGGGAAATGAGCAGTTGGCAGTTCTGTATTTTGTAGCCGCTAATATGTTGATCAAACATGTCACTGACTGCTTTCATGGAACTGAAGTTTCGTTCAAACATCAAAGCTTTCGCGAATTGGGGTAGGAAGAAGTGACGCCACCGCTGCCCACATGGGTTTGTATTCATCTTGGCATCTAACTGTTGGTAGAGTCTGATCAATGCTGAACAAAGGTCCGCATGTAGAATACCACCGCGGATGACCTGCATTTTGATTTCCTTGGCACTTATCTCAATTGATGTAGGCTTGTCGTGCTTGAACCAAACCCCGGTTATATCGTCATCACATGACTCCTCAAGCCAACGGAATAATCTCCCAGCTAATATAGAGTTTGGCCACCATTCATGAACTGTGCGCATTGAAAACGATGACATGCAAGATGGCCTTAGATGATTCCCCGCCTCTTTCGTCATCTGCGTCTCGCAACGTTCTGATTGCCCTTGGTACTTATCCTGTGCACCATTGTTGTTTTGATCCAATGTGGCGCCGTCTCTCATGTTAGCTTCTCCCACAGCAGCTGCTGATACCAACCAATCGAGGAAACATTTGTCTTGCGTTTGGAAAACTGTGTTTTGGACTTGATCCAACCCACGATGGTTTGTATGAACTGCTGACGTCGCTTGGGCTGGTGATTTTAATAGATGGTGATGTGCGATACGGGCCGTGCGTGACACCGACAACGGATTTGCACGGTCAGCAGCTGGATTTTGCTGCCCTCTTGCTGCATTTGCCAATTTGTTTGGCCCTAACAAGTCACCTTTGCCTCTCAAATCAATGGGGGTTTGGGATCTATTTGCTGCAGAAGCCTCATGTGACAACTTGCTTCGTTTACGAGTAGTCTTGGCACCTTCACCATGTGATGCAGTTCTTCGCATCGTTGCTGCTAGCATATCGTCAGTATCCACACCTTCGATTGCGCCATGTAATCGAGCGTTGGATCGATCGGGATTTGCTTGGACAGCTTGATCCATTACAGCCGAGTAACATTTCTCACCGTGTTCCGCTGCCAAAGCCTGCATGCCTTCCGTTAAAGATGAAAAAACGAGGCCGCATTTCTCGTTGTGCTTCGCTAACAATGCCAGAATGCCTTCCTGCGTTGCCTGAAATGAATCTTTGATCTCTGCCATGGCCTCATCCAACATCTGCGTGCATCGTTCGCCAAAATGACGCGATAGATCGGACAGCTTGGCAGGCAGGTCGTTGCCATGGCTATCGCTATTGCTCGGGTCAGTGTCGTCGTCGTCCGAAACGTCTATGGGCTCCTCGTAAGCATCACACCGAGCTTTACCTTTGCCCTTCATTGATGAAGAAACAACTGACTCAACAACATTTTTTCGCTTCAAAATGGAGTACTACGCAGTAATACGCTTAGCTTTGATCTCTACCGTCTTAGTAAAGCACAATCGTATTTTTTCCCTTCCCACTGAAAAACCGCTGAAAAAAATCCATTGTATATAAAAAAAAGAGACCAAACCTAAAGAGATTCTGAAAAAGAGAGAAAAGAAAGAATCACGTTCAGCAGATCCCGTCCCGTTGCAATGCTTGAGCCCGAGGCAGCCTGTGACTACTCCCTCCGTCCCTCCCAAACTAATAAGCGTGTGTTTGGTTTGGGGACAAAGTGGGATGGGTTAGACCTATCCCAGTTTTTTAGGATGGGATAGTTCCAGTTGTCTGTTTGGTTTGTGGTATGGGATGGTTATAGTTTTTTGTTTGGTAGAAGGGATTGAGGTGGGATGGGATGGAGAACTTTCACGGACCGTTAGGGCCGTCTGGCTCCCAGCGGCTACCTCGCAGACGAGCGGCGGCGGTCGTTCACAGAGGCGGAGGAGGTTGCAGACGAGGCGGCGGCTGGACGCGGAGGCGCGCGCGGCGGCAGTCGCGGACGAGGCGGCGGCTGCGCACGGAGGCGGAGGCGGTCGCGGAGGCGAGGCGAGGCCCGGACGAGCGGCGGCAGTCGGTCGCGGAGGCGGAGGCGGAGGCGGTTGAGGACGAGGCGGCGGCCGGACGCGGAGGTGGCGGCGGTCGCGGACGAGGCGGCAGCCGCTCACGGAGGCGGAGGCGAGGAGAGGCGCGGATGAG

Coding Potentia
Explanation CPC Score
noncoding -1.13512
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0320900.2 5 27960235 G A
Osa05LNT0320900.2 5 27961315 G A
Osa05LNT0320900.2 5 27958502 T C
Osa05LNT0320900.2 5 27958572 G A
Osa05LNT0320900.2 5 27959045 A C
Osa05LNT0320900.2 5 27960290 G A
Osa05LNT0320900.2 5 27960627 T C
Osa05LNT0320900.2 5 27960675 A C
Osa05LNT0320900.2 5 27961814 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
Osa05LNT0320900.2 osa-miR5526 Cleavage 4.0 19.63 1 21
Osa05LNT0320900.2 osa-miR1437b-5p Cleavage 4.5 24.542 1 21
Osa05LNT0320900.2 osa-miR418 Cleavage 3.5 15.391 1 21
Osa05LNT0320900.2 osa-miR530-3p Cleavage 4.5 16.148 1 21
Osa05LNT0320900.2 osa-miR1846d-3p Translation 5.0 12.154 1 20
Osa05LNT0320900.2 osa-miR2926 Translation 4.5 21.718 1 20
Osa05LNT0320900.2 osa-miR2926 Translation 5.0 15.906 1 20
Osa05LNT0320900.2 osa-miR395x Cleavage 4.5 20.143 1 21
Osa05LNT0320900.2 osa-miR5160 Translation 4.5 18.5 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0320900.2 5 QPl5 Morphological trait Panicle/flower RG13 RG346
Osa05LNT0320900.2 5 QFla5 Morphological trait Culm/leaf RG470 RG346
Osa05LNT0320900.2 5 nan Physiological trait Eating quality C246 C1447
Osa05LNT0320900.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0320900.2 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0320900.2 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0320900.2 5 tp5b Morphological trait Culm/leaf RM26 C1447
Osa05LNT0320900.2 5 qMRL5-1 Morphological trait Shoot/Seedling RM26 C1447
Osa05LNT0320900.2 5 qTDW5-1 Morphological trait Shoot/Seedling RM26 C1447
Osa05LNT0320900.2 5 qRFC-5 Physiological trait Eating quality RG470 RG474
Osa05LNT0320900.2 5 qRSd5 Resistance or Tolerance Other soil stress tolerance C1447 RM26
Osa05LNT0320900.2 5 qRNw5 Resistance or Tolerance Other soil stress tolerance C1447 RM26
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