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

>Osa04LNT0279600.2

TGAAATTACGATATAAGAAAAGGGACTGTTGTTTTGAAGATGCTGACACGGTGACACCAACACACACGAACACATATTGTTGTTTTCAAATTTCAAACATGCCATCTGCAAGATTGGAAGTGAAATGGAACACAGTGGAAGACCAACCACATTACTCTCCCAATTACTCTCCTAACAACTCAAAGAAGGACCAAAGAAAGCTGCTATCATGCGTGACCAACCAACTAAATGGAAAACGCAGATGCAGCATATCTGAGATCCTTGCGACGCCTGCACGATCAGCATGCTAGGATGTGAGTAATACTTCCACTGTGTACTCGAGCATCCACCAACCAGGTTCAACCCGTGAGGCAATCATCGAGTTTGTTGGCTAGAAGAGTTAGGGTTGTACAGCACAGAGTAATCAATATAGGGGGACTGCAAATCATCACGAGAGCTCGATGCATTTTGGCCCTGTGGAAAACTTGGAGGCGCCGTTGATGCACCCATCAATCCATCAGGCAAACCACCATTTGACATCATTTTCTGCATGGCGCTCACTGTATTCCTCATGTTAGCCAAATCCTCCTGCAGCTTTTTCTGACTTTCCTCCATTACCATCATCTTCTTCCTCAGTGTGGCAGCCTCATTTTCAGCAATCTCTTTTGCATCCACAGCTTCCTTGAAGGATGCCTTAAGGGCTGCCTTTTCCTTCAGGCCACTAGGGCTGGCCCCAGGTTCATGGTTATGCATCCTACCCCTCCTCTTTTCACCCATGGCTGTGACATCATCACTGCGCTTACGAGCCTTGTCACGAGAACATGACTAGACGGAGAAAGAAATGTCAGTTCTTTTACACTTCAAAAGGTCAAGTACAAAATAAGAGTACGAATTTATACACATGTGAAATATAGTAATGGACTCTTCGTCAAGTATCCGTGCAAAGCTCTTCGATCCTGTAGAGCTGATATAGGTTGATTTTGCTCGAGAAGCTTTGCATCTAGCACTTGCAGCCTGTGCCTCTTCGGTATTCCAAAATGCAACAAGGAATCGCCACTGTTCTTTTAGGACACGAGGATCACAATCAGCAAGACGTTCCTCTTCAGTTATATGAGAATCATAGTGTTTTCGTTTTAAGTTACACCTCCAATTCCTCCACTTTGTTCTTATGCATTTCAGTAGCAAGGACTCGGAAGATGGAGCAACATAAAATTTAAGCTTAATAATATGCCACATTACATCCTTGTTCTCCTTTGGTATACTTTTCCATTTTTTATATGTAAGAGGTGCCAATATTCCATCACGCGCTAGTGTGCCCAGAAAGTTACCAAACATGGCAGCATTTTTTCCAATAGGAAAACCTGAATTGTTCAAGGATACTGGAAGCCGCACACCTTCAGGCAAGGTCCACACTTTGACACAAAGGGTAGGGCCACGCCTGTGTCCTTTCTTTCTCTTGCTACCAATATTCTGGCCAGATGGCTTCTGACAATCACGTGCTTGCTCCGCATCAGGAAAATCATGCACAAATTCCTCATCGGAACATTCCTCGGAGACTAGATGATTAAGTAATGAATTAGATCTTTTCTTTGAAAGGGCCCTTCTGACCTCTAGAGGGAATACCTGACAGTAATGTTGAGCAAAACGCTCAGGATCAGACATATCAGGATTTGAAGGAGTTGTGGCTAAATCAGGGTCATCTGGTTCACTAGATATTTCCCGAGGCTTCTCATGAACAGAGGATGTGCTAGGGCAAAGACCAGCAATGATTCTGTCAATGTCTGGAGGGTCAGACATGCTTTGATGTGGAGAAAAAGCACAATGCTCGTGATGCTCACTTTCTACAGATTCGGCGTCTGTCGTAGATACTAAAACTTCACAATTTGGAGAAGGAGACTGATGCAGAATAGGCTCCTGTTCTATTGGTTCACTAGACATAGCAACCGCCGACACCTGGCAATTCGGAGAAGAAACCTGCAGGTCAACAGGGTCATTTTCAACTGGTTCATTTTCTACAACAGCAACTGAATCTTTGGCCAAACGTTTACTACGCCTAAGATGAAGACTTGAATTTGAAGAAGCCATCAGCCCCTTCCTGTTCTTCTCCCGGGCTTGACTAGAAGGCTGCTTGCAATTTTCGACATTAATATGCTTCTTCTGAGCCTCATGATTGGGGGGCATGTGTTTCTGATTTATATGGCTAAGCTGATTCGGAGAGACTAGCAGATCCTGGTTCTTTAGGGTCAAATTAGAGTCAACTCCAGTTCCAGTTTTTGGTTTGCCTTTTCTTCCAATATGCTTACTCTGAGGATCAAAATCCACCTGCATTGCATGATTATTAATATCAGAGGTATGTCCTGTGTGCTGTATAACATGGCTCAGTGGCTCTATCTGTCTCTTGTTAACATTATTTTTAGGATCAACTACGTGTACAATGTCCTGCTCGCTATGCCTTGCAGAAGAATCTTTTCTGGGTCGAAAGCACATGGCTTCTCTATGAGTCGTTTGACTTACATCCTCGTGAATTTCCTGATCTGGATGCTCTATCTGTGCATGTTCTGCATCATTAGCATAAGATTGATTTGTTTGTGTCTGCTTTGTGACCTGATCGGCGGTCGATGTTTTTCTCTTCCCTGCACTAACAGTGTTATGTCTAACTGAGCATCCAGATTTCCAACTGTCACCCCTTGCAGTTGTTTTATCTATAACCTGAATGCATCCCTCTTCTCCATGATTTGCTTGGTCAACAGGTTCCGGTTGCGCCTCCTCTGCATGAATCGCACCATCTAGACACCCTACCTGAGTGTGCTCTGCACGAATTGCATGAGCAGTATGCTTTTGCCGCTTCTGTGTGATCTGATTATCGTGTTCAATACGCCTCTTATCTACACTCCCAACAGCTTCGGGGGCAACAGAGCACATAATTCTCCGGTTGCTATGAGTTGTAGCAGTCTCATATATCAGTTCAGCATGGCTTGCTTCTCTATAAACTTCATGGCTAAGAGGCCCCTCCTGTACCTCCTCTGAATGAATGACTCTATGCAGGCGTGCTAGTTGTGCCGGCTTTCGCTGAGTACCGTAGCTTGAACGCTGATCATGTACCTGATGCCTGGCCGCTTTTATCGGCAACAACCTATTCTTCACACTTACAATACCAGGTTCAACTGAACATCGGTTCCTCTGCTGGATATTACTTGAAACAATCTCATGAGCTTCCTCTCCACCAAACACACCATCAGGATACTCTTCTTCATCCTGCTGTAGATGAATAAGACGATCGGGATGCTGTATCCGTGACCGTTCAAGAGGAAATAGTCTATCATCAGCTTCTGCTCGGGCAAATCCTGAACGAACTGCAGAATTAGGGCGCCTTTGCCATGCCTCCCGGCCACCGAGGATGGGTTGCGCGGGGGCGGGGGCGACCGGCACCGGCACCGGCACGGCGGCCGTCGCGGCGGAGGACAGGATGTAGTTCCGGAGCCGCGCGGGGTAGACGGCGAGCTCGGCGCCGCAGAGCGGGCAGGCGCAGCGCGACAGCCCGACGGGGACGCTCAGGAGCTCGCCGCAGGAGCCGCAGGGCAGCCGCGCCCCGCGCGCGTCCGCGGCACCCCGGGGGAGGGGCAGCGCCCTCCGCCGCGGCGGCGGCGGGGCCGGCATGAGATCCGGCGGGAGCGACTGCGGCGTGGCGCAGTCCGGGCAGACGAACTCCGTCAGCCCCCGCTCCACCTCCAGCGTCTCCCCGCACCCCGCGCACCCCACCTCCAGGATCTCGTCGGGTTCCTCGTCAGCTGCTGCCACCGCCATCGCCACCGGCGGCGGCGGCGGCGCCATTGCCTTCAGCCCTCAGCGCAGTAGCGTCGGAGTGTGGAGGCGAAC

Coding Potentia
Explanation CPC Score
noncoding -1.20068
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0279600.2 4 30910933 G A
Osa04LNT0279600.2 4 30910966 A T
Osa04LNT0279600.2 4 30911398 T G
Osa04LNT0279600.2 4 30911426 A G
Osa04LNT0279600.2 4 30911514 G A
Osa04LNT0279600.2 4 30912162 G T
Osa04LNT0279600.2 4 30912401 T C
Osa04LNT0279600.2 4 30909261 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0279600.2 osa-miR5827 Translation 2.5 17.317 1 21
Osa04LNT0279600.2 osa-miR396a-3p Cleavage 5.0 19.969 1 20
Osa04LNT0279600.2 osa-miR396b-3p Cleavage 5.0 19.969 1 20
Osa04LNT0279600.2 osa-miR396c-3p Cleavage 5.0 5.95 1 21
Osa04LNT0279600.2 osa-miR396c-3p Cleavage 5.0 19.969 1 21
Osa04LNT0279600.2 osa-miR169f.2 Cleavage 4.5 13.233 1 21
Osa04LNT0279600.2 osa-miR2878-3p Translation 4.5 9.081 1 24
Osa04LNT0279600.2 osa-miR5082 Translation 5.0 20.586 1 24
Osa04LNT0279600.2 osa-miR5509 Cleavage 4.0 16.823 1 21
Osa04LNT0279600.2 osa-miR5515 Cleavage 5.0 21.496 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0279600.2 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0279600.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0279600.2 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0279600.2 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0279600.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0279600.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0279600.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0279600.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0279600.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
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