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

>Osa01LNT0039000.1

GGAAGTAAATTCCAATTTTCCAATAGATGTACGTCAACCCTTTGCTTCCTCTCCAGCTGCAGAGTTGCAGGTTTGACGAATGCAGCTTATCTACAAAATTCCCATCAGAGGGAACACAGTTACAGAAGAACTAGGGGAAGTACAGATTGCAAATCCATAAGGATCTTCTTTAGAACCGTATACGTAAAGGGCTTCATGGATTGGCCACTATATATGGGTGTCACCCTCAATCGTGAATCTGCAAGGTCAGATATCAGTATATCAAATGCAGATTGCCTCATTGCAGATTGCTGTGGATTGTTCAGGTTCCGGGTTAGCCCAGTCACCAGTCTTCACTGACATTAGCCCGCTGTGGTTACATCAGATAGTAACAAGCTCCTTCATCATTTCGGAATTCAGTCGGTGGTAAGGCATCGGAAATGGCATCAAAACAACTCTTGCTGCCTACCTTTCAGCTATCCGTGCTGCCATCATCGTCATCTTCATCCCCAGAAGCTTCATAACGTGGCTGATCATACTTCTCACGAAGCTGCTTGATAGGAATGAAGTCCCCAGCAGTGTCCTCGCCAAAAAACAGAAATTCAATATAGGGGTGATCAAATCTTCCTTTCTCTGATATTTCAGCTTCTGCAAGATTTTCTTCTGCAACTGAAATTACACAGACATAACATGTCTCAAAATGGCGCAGCATAGGCATAAAACAGTAAGTGAAGATGGATTTGATCAATTGACTACTGCATAGCCTACTATCTTGCCTTCTTCTGCCATTTTACACAAAACAAGATTGCTCATTAAAAGTTACAGATCTCAAGATAGAATTTCCACCAGTGGTCATGTCTATCAAAATAGTGGAAAAGAAAAATCAATACCATATGCAACAAGGAGTTCTGGATCAGCATATACATCAACAAGGACTTGATAAAAAGGTTGATTCGGTCCTTTGGACAAGTTTTCCACATTTGCTGTCTCCATCCATGACTTGGATTCACAGCACACAGGATCCATGCCACAAATCACAGCTCTATATCCTTATGACGTACTTTCTGCCCTAGTCGAAATGCATATTCCACATTTTGATATGCAAGGGCCTTAGCGGAGACTGCCAGAGACTCTGTCTCAAGTTTAGCAATTTCATCACGCAGTGCAGCTGCCAAAGCATAATTTTCACTGTCAACAGCCTTTTGCAAATCCGCACGCACGCGTAAAAGGTTTATAGCTTTGTCCTGAGCTTCAGTCTTTGATGAGCCTCTTTTAGCTTCACGTTGCCTAATTATCTCTGTTTCAATCTCTGTGAGTTTTTCCCTCAATTGTTTTGCCACATCAAATTGCTCTATATTCAATGCATACTGTATTCGGGTTTGTAGGTCCAATTGGAAGTAGAAGATTAAGATGTCTTCGTTAGCAGACTCACTGCGTTCCAGCCTTGCATTACTACTGCTACGGTCATCTCCTCCAAATAGCCATTTAGCGTTAGTTCTCACTGTAGTACCCATTTGCCTTCTATTGGTCCTCATATGTAGTTTTTTCACACACCAACGCCATGAGTACGCTCCACATGTTATTGAATTTATTTTGTAAAACAACCTCAGATCATCCACTGCAAGACAAGCTGGTCTAAAACATGATCCATGGGGCGAGGAAATTGAACCACATGCAAAAATGCCTTGCATTGTATTGGTATGAGATTTGACCAGTTCAATTCCCACAACTGATGTAGTCCAATCACCACACTGACAGTTGCAATCAGCAAGCCAGTGGCATCTCCAGCTTTTCTGGCCGAGGCGGCGCGCGCTTCGGTGGGAGGAGGAGGCGGGGAAGCGTCGACGAGTCTCGGCGAACGGGGAAGAAAGGGGGAGGGCCGCGCGCTTCTCGGCCGTAACTACCACTGGCTCAAAGTGTGGCGGTCGTCGACGGGATACCGGATAGAATGTGTGACCTGGATCAGGAGTGCATCGACTGCAGGTTAAGCACTTGGGTGAAACTGACCGTCCAAGAACCAGCGAACGTTTAGGATTCTCTGACCTCGCCTTCTCCTTCCCTTCCCTTCATCAAGATTTGGTTACAATTTTGGGGCAATTGCATCTACGCCCCCACTTTCAAACCCAATTGCTGTTTTATCTTCACTTTTTAGGGACATGTATACCCTCTGCATCCAGCAATATCGTGCAGGGGAGGACCTGGAACAAGGGACGGGGAGGAGGGCGCCGTAGGCGCCGACGTCGACGTCGAGCAGGATGGGGTCGTCGCCGGCCACGGGAGCAGTAGCAGCAAAAGCGATGGTGGGGGCAGGCGGAGGCGGGGGCTGACGACGATGCCTCGGCGTGGAAGCCAGCGGCCACGGGAGCAGCAGCAGCAGCCGCCGCCGTCGCCCGCACGCCGTTGCCGCGCGCACGCCCTCGCCGCCGCCCGCCCTCGCCGCGGCTGCC

Coding Potentia
Explanation CPC Score
noncoding -1.07641
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0039000.1 1 32178674 C T
Osa01LNT0039000.1 1 32179117 T A
Osa01LNT0039000.1 1 32179648 A G
Osa01LNT0039000.1 1 32179615 G A
Osa01LNT0039000.1 1 32179202 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0039000.1 DTM_#DNAt_MULE_japo_Os0709 Chr1 - 32181320 32183575 356
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0039000.1 osa-miR5796 Cleavage 5.0 16.613 1 21
Osa01LNT0039000.1 osa-miR395u Translation 3.5 9.413 1 21
Osa01LNT0039000.1 osa-miR166g-5p Translation 4.0 14.138 1 21
Osa01LNT0039000.1 osa-miR166g-5p Cleavage 5.0 20.589 1 21
Osa01LNT0039000.1 osa-miR417 Cleavage 4.0 17.576 1 21
Osa01LNT0039000.1 osa-miR417 Translation 4.5 21.18 1 21
Osa01LNT0039000.1 osa-miR1439 Translation 5.0 15.993 1 21
Osa01LNT0039000.1 osa-miR1854-5p Translation 4.5 18.623 1 21
Osa01LNT0039000.1 osa-miR2093-5p Cleavage 4.5 11.016 1 20
Osa01LNT0039000.1 osa-miR5082 Cleavage 3.0 18.545 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0039000.1 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0039000.1 1 qCC-1 Physiological trait Source activity RG541 RG101
Osa01LNT0039000.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0039000.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0039000.1 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0039000.1 1 gpy1 Others Others RG541 RG101
Osa01LNT0039000.1 1 nan Physiological trait Source activity RG532 RM472
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