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

>Osa01LNT0040600.2

GACGCCGACTTTTACCGGCAAAAAAACATTGCACACATTTTGCATGAAACTGATACATCCCTCTGTACAGAATTGTCTACACATCAGATTTTTTTTTATGGGGCGAGGAATCTACACATCAGATTAAGACTAACTAATCACCTGTTATGATTCTTACTAATTACATGCGCCTAGCTAGCCATCATCTTGTTCGTCGATCGTCTTCGTTTCAGGACTCCGCCAAGAGCGGCGGCGAGTCGAAGATTCCCTGGCCGGTGGCGAGCATGGCCCGCGGGTCGAACTCGGCCTTGAGCCGCGCGAACCGAGCCCACCTCGCTCCGAAATGGGCCTCCCACTCGCGCTGCGCCTTGTGGTTGGGCAGGTACTGCTTGGCCCCGATGCCGGCCTCGTCGCAGAACTCGAGGATCTCCCGGTTCTGCCGCTCCAGCGCCTCCAGGCTCTGCGCCGGGTCGGTCGAGCCCGGCACCGCCGACCGCAGGAACGCCACCAGGTAGAACACGTCCTCCTCCGGCGTCACCACCGAGCTCCTCGGGTCCCACCTGCAACGTACGCAAATCAAGTTCTCTTTAGTATTTAAATCCACCGAGAAAAAAAAAGAGAGAGGAAAGATTGGAGCAGAGTAGGAAAAGCAACAACAGTTAGCAGCAAGATCTGTGCTGATTCTGATCGACACGTCCTTTCAGGTTAAGTACTAATGTGAAAGCGACAACACATATGTGCAATCTGGCCACTAGCGAAGCTTAACAACTGGTGCCGTGGAAAGGCGATTGGGAACGGGAGCGGCGCGCGCCCTGGTTAGAATAACCGGTCGGCGCAAGGCGGTGAAGGTGACTGATGATGCGCCCGCCCCCCGTCTGTTCTGTTCTGTTCCTAGCATTGGCATGGCGCCACCACGCAGCGATTAGAATAGGGCCCTGTCGCCCTAGTGCGCGGTATGTCCGCGGCCAATTCCAGTCACCGGAGATGCGGCGGCTGCGTTTCGGAATTAAAGTATGGCGGCAGCACGATCCATCCTGTGCAATCTGCTGCCCATCTGGAGGTATATTTGTTTATCCCGCGCCAATCATGGGACGCTCTCTCTCGCGCGCGCGCGGGCGCGCACGCCGCAGCCCATCGGCCACCTGCCCGCGCCCTCCCGTGTTGCGCCGCATGTGAGAGGACGGCCGCGCTTCATGTGACGTTGTGCCTGTTCATGGGGTAGATGAGGATGGGGCCACCGGCGGTGCGGCTGCCGAGGACGCCGCGGAAGACGCCGCGGTCGAAGTCGGCGATGCGGGACGCCGGCACGAAGAGGTTGAGCCACGGGTGCGGGACCTCCCACATGCCCTTGCCGCGGAGCTTCAGCTCCGCCTTGTGCACGCGGTCTAGGAAGTCCACGTACGGCAGGTCCGTCGTGAACACCGTGCCCGGGATGAAATTCAGCTCGCCCAGCAGCGCCTCCACGTCCTGGTCGACGGTTACGGCGGTGGAGTCGTCGTAATTCTTGGTGACCTCCAGGCAGTAGAGAACCCCGGAGTGGTGCTTGAGCGAGCTGAGCTTGACCGGGTTCTGCGGCGAGAAGAAGGACGACCTCCAGTTGTTGATTAGGCCCTCGGCGGCGACGACGAAGCCCTCCACGTAGTCGAACCGCCGGCCGCCGTGCTGCAGGGAGATGAGCCGCTCCTGGTCCGCGGTGAACTCGGTGAAGTTGGAGTAGAGCGCCCGGATCCAGCGAACCTGGCAATGCAGGTCAGAACGACAAATTAATAAATTATTATTACCCACGGGCCGTACCGATCATATGGACACAGCTTAATCAGCGTTAGATCACACACGCTTAGTTAGCATGGATTAGTTAGCTAATTGAGCTGCATATGACAACAAAATCTTGTGAGTGATCGCACGATCAGCTAACCAAACGCTTCTATATAGAGTATATTTATAAGCAGACCACCAATTGGTCAGCACAAACTATTCGGTCGATCCATCGGGTCGGCCCCAAATTCCCAACCAACCTGGTCCACTACCTGACCCGACGCGCACACAAAAAAAAAAATCCCATCTCCAGACGCTTTTTCTCGGAGACCGTAGACCTCAACAGCGACCCAACATAAAGTTAACACTACCCCCTGCTCGGTCGCTGGTCGATCGATCCTGTCCTACGTGTCAGCTCCCAACGGTGACTTTCCTTTGCGACGGCCACAATTGGCAACACGTTTCAATTGGGTGCCCCGTGCCCCTTTGTGGGGTTTCGATCGACATGTGGTGAAATTGCGGTACTTAACAAAAAGATCCCCCGAGAGGCCATCAGCCAGCCCAGCAGCGCGCATCAATCGCTCGCTTTCCCTCGCGCGGCGTGGCGCGCCCGGCCGCCACTTGCATGGCTGCTCGCTGATGCCTCAGTTCCCTATTGGGCCATTA

Coding Potentia
Explanation CPC Score
noncoding -1.22178
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0040600.2 1 32789283 C T
Osa01LNT0040600.2 1 32789506 A G
Osa01LNT0040600.2 1 32789626 T C
Osa01LNT0040600.2 1 32790477 T C
Osa01LNT0040600.2 1 32790918 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
Osa01LNT0040600.2 osa-miR7692-3p Translation 5.0 21.481 1 24
Osa01LNT0040600.2 osa-miR171a Translation 4.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171b Translation 3.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171c-3p Translation 3.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171d-3p Translation 3.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171e-3p Translation 3.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171f-3p Translation 3.5 18.839 1 21
Osa01LNT0040600.2 osa-miR171i-3p Translation 4.5 18.839 1 21
Osa01LNT0040600.2 osa-miR820a Cleavage 4.0 23.338 1 21
Osa01LNT0040600.2 osa-miR820b Cleavage 4.0 23.338 1 21
Osa01LNT0040600.2 osa-miR820c Cleavage 4.0 23.338 1 21
Osa01LNT0040600.2 osa-miR1440a Cleavage 4.5 23.6 1 20
Osa01LNT0040600.2 osa-miR1851 Cleavage 5.0 11.209 1 21
Osa01LNT0040600.2 osa-miR5074 Cleavage 4.0 17.713 1 21
Osa01LNT0040600.2 osa-miR5146 Cleavage 4.5 24.109 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0040600.2 1 qCC-1 Physiological trait Source activity RG541 RG101
Osa01LNT0040600.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0040600.2 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0040600.2 1 qLRC-1 Resistance or Tolerance Drought tolerance RM237 RM302
Osa01LNT0040600.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0040600.2 1 gpy1 Others Others RG541 RG101
Osa01LNT0040600.2 1 An10 Morphological trait Panicle/flower nan nan
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