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

>Osa09LNT0450200.2

GAAAAATGATGGTGAAAACATTTTGCTCCGAATAGCTTATACATTTGCTTTACTTCCATTTGAAATGCCAAACCGTATTATCATTCAAAAAATGAATCAGCACACAATATTTTGTACTGATGTTTCTAAAAAGTATCGCGCAGTAAACTCTGCAGGTAAAAAAATAGGCAAAATGTTGCACCATATCAGCTGACTCGAGAACAAAATATGTATGATGTAATAAAACTGTAAAACTTGGCTATCTTCTGTCAGACAGAAACTCATATCCACTCTACCGAATCATGCAGGCCATCTGATTCGTCAGATGTTCTCTTGATTTTCTCTCAAAACCTGGAAAACATCGCAGTTCCTCATGAATGGATCATGTGGTGATGGGTATTTGAAATGGTCACTCCGGAGCTTTTGTTGCGCAGATCATGTACTGGCAACCACCCCTTGCTCAGAAAGAGGTACAGATGGCCTCCAAGTTGTTCCGTCAGGACCGTCCATGAGGGCAATTCCAACAGCAGCCAATTCTTTTCTGATTTCATCGGATTTTTCATACTGTTTTGCCTTTCTTGCTGAAGTCCTTTCTTCAATTTTCTGAAGCACCTGCTCCTCTGTCATGGAAGCTCTTCTTAGTGCTTTTTCCCGCAGCTGCTGCAGAGCCTCATAATAGCTTGATGGTAGTAGCCCTAGGACAGAAAGCACCATCCTTATTTTCTCTTCCATAGCAGAAAGTGATTCCAGCCGTTTTTCCTGCTTCTTTCCCTTACGAGTATGCAGCAAGTCATTCATAACTTTTAATGGCTCAGAAATAGCAGCCAGTGCTACTGAAGTGTGAAGATCATCAGACATTGAAGTCTCAAATTCATCATGGAGCTTCTGGATACAATTTGTAGTATTAACAGGTAATGGATCTCCAGCCTTGCTTTGGTGCTGTTGACAACTTTCTTCACAATCTTGTAGTGTCTGTAAATTAAAAACAAAAAACATAAACTCTTTAATTAAGAGTTATGGCATTGAAATATCTCCTGAAGAAACAGCAAAAATGCAGCATCTCCCTTTCAGTGCCACCAAAACTCAAAAGTTCTGACTAGTCATTCAAATTGAAGCAGCTTCCCAGTCTCCAGGCATAAAGGTTAAACCAGAACTTAAGTGATCTTGCTTTGGCTAGAGATTGAGAAGCAGCAAAAGCCAGGGCTGCCTGGTCAGACCATGCGTGCAACTATAGCTATACTAAGATGAATTCAGTGCTACCCTGTGATTCTAAATTTCGGGCCAATTCACAACCAGTTTTTAATCAGCTAAGACAAAAAAAAAAAGTTCAATGGACATTTCAATTTAAGCGAACCGACTTTTATTTGGAGTACTGCAGCTTAGCCAAGACAAGTGCAGATGGCAAGTTGTATGGGGTTAAGGAATGAATCATGGTCACAGACTCACAGGCCATCTGAATAATGATATATTTGGCTTTCAAAAGATAAAAATATGGTTCATCTAATTAATATATCTATAGACTAAATGTGTATCTTAATCTTGTAAATGCCTTGGCATAAACATAACCTACACTTGTTCTCACAAAAAAAATTAAGTAATGTTACTAATTCATGCATGCCAATTTAAGGTCCAGTGTCATTCCCTCTTTAGTTTTTACAGTAGCATAGACACTTTTGGAATGTGAATTTACAGATGCTTTTAACAAGGCAAGCCAAAGTACAAAGGCCTGAATAAGTCCTAGAAGCCAAATAGGCTCAGGATCATCTTTCCACCACCCCAAGGTCCGGCCCGACTGTTTTGAGTCTGTCTGATGCAACATTAAGCTGTTCTATGGTATAGTTGATTGGGGACCTGTAGTGTGTACCAAGTAAAAACATCCTCAAAGCAAGTGGGTGGTACAGTTCCGTAACTTTGCGTATAGTGACAAAGTTGCCCAGCGATTTTGACATTTTCTGGCTGTTTACATTGACAAAGCCATTGTGTATCCAGTAATTTATGCTGCTGTCACAACATGCTGCACGGCTCTGAGCAATTTCATTTTCATGGTGTGGAAAGATCAGGTCCTCCCCACCGCCATGTATGTCGAAAGAGTGGCCCAAGTAATGTGCACTCATAGCACTGCATTCTATGTGCCATCCTGGCCTTCCAGGGCCCCAAGGGCTATCCCAAGATGGCTCCCCATCTTTTGCAGCCTTCCAAAGAGCAAAATCAGCTGGGTTCTTCTTCCTCTCATCAACAGCAACCCTTTCACCAGCTCTATTATCATCTAATTTTCGACCAGATAAATCCCCATATTCAGGGAAATTTTCAACAGAGAAATAAACATCCCCGCCAATTGCATATGCACAATCATTATCAATGATCTGTTTAATCATGTTTATAATCTGATCAATGTGGTCTGAAACGCGAGGCTCCACAGATGGTGGTAAACAATGAAGATTAGCCATGTCTGATAGGAAGTCATCAGAGTACCTTTTGCTTAAGCTAAAAGGATCTTCTCCCAATTGATTTGCTCTTGCAATTATCTTGTCATCAATGTCAGTAAAATTCCGAACATAGCGCACTTTATGGTCCAAATAACGCAAGTACCTGTAGAGGACGTCGAAGGCGACGTAGGCGCGGGCGTGGCCGATGTGGCTGTCGTCGTAGGGGGTGACGCCGCAGACGTACATGCCGACCTCCCCGCCGGGCACCCGGGGCTGGAAGAGCTCCTTCCTCCGCGACTTGGTGTTGTAGAGGTGCAGCTCCCGGGCTCTCCCCGCAGGCGCGCCATTCGAGGCGGAGGCGAAGGCGGAAAACGCGGCGGACGACGAGGGCTTGGGGGAGTGGGAGTAGAGGCGGTGGGGGCGAAGCAGAGGAGGGGTCAGGGCAAGCGCTTGGCGGTGCGGTAGGCGAGCTCGCGACGGCGAGGAGAGGAGGAGAGGGAGGAGGCCAGCGGCGCGCCTCGCCGCCGCCATGGTCGGTCCTCGAGGCACAGGAAGCGCGACGGCGCGAGGGGTTAGCGGATAGCGTTTCCCTCTTT

Coding Potentia
Explanation CPC Score
noncoding -1.00495
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0450200.2 9 22114977 A G
Osa09LNT0450200.2 9 22115482 T C
Osa09LNT0450200.2 9 22115857 G A
Osa09LNT0450200.2 9 22116111 T A
Osa09LNT0450200.2 9 22116195 C G
Osa09LNT0450200.2 9 22117176 T A
Osa09LNT0450200.2 9 22117794 T A
Osa09LNT0450200.2 9 22117856 G A
Osa09LNT0450200.2 9 22118093 C A
Osa09LNT0450200.2 9 22118258 G A
Osa09LNT0450200.2 9 22118439 G A
Osa09LNT0450200.2 9 22118679 T G
Osa09LNT0450200.2 9 22119385 C T
Osa09LNT0450200.2 9 22116420 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0450200.2 osa-miR5534b Cleavage 5.0 18.104 1 21
Osa09LNT0450200.2 osa-miR5542 Translation 4.0 19.849 1 21
Osa09LNT0450200.2 osa-miR5831 Cleavage 5.0 19.434 1 24
Osa09LNT0450200.2 osa-miR5832 Translation 4.0 5.267 1 21
Osa09LNT0450200.2 osa-miR5512b Translation 4.0 12.214 1 21
Osa09LNT0450200.2 osa-miR820a Cleavage 5.0 18.153 1 21
Osa09LNT0450200.2 osa-miR820b Cleavage 5.0 18.153 1 21
Osa09LNT0450200.2 osa-miR820c Cleavage 5.0 18.153 1 21
Osa09LNT0450200.2 osa-miR1848 Translation 3.5 20.419 1 21
Osa09LNT0450200.2 osa-miR1874-5p Translation 5.0 24.138 1 24
Osa09LNT0450200.2 osa-miR2093-5p Cleavage 4.0 9.412 1 20
Osa09LNT0450200.2 osa-miR2093-5p Cleavage 5.0 15.562 1 20
Osa09LNT0450200.2 osa-miR2094-3p Translation 5.0 15.725 1 22
Osa09LNT0450200.2 osa-miR5076 Translation 4.0 9.483 1 22
Osa09LNT0450200.2 osa-miR5083 Translation 4.5 14.567 1 20
Osa09LNT0450200.2 osa-miR5489 Translation 4.5 17.357 1 21
Osa09LNT0450200.2 osa-miR5504 Translation 5.0 10.547 1 21
Osa09LNT0450200.2 osa-miR5508 Cleavage 5.0 12.003 1 21
Osa09LNT0450200.2 osa-miR5512a Translation 4.0 12.214 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0450200.2 9 yldp9.1 Morphological trait Seed RM242 RM205
Osa09LNT0450200.2 9 qTN-9-2 Morphological trait Culm/leaf RM215 RZ404
Osa09LNT0450200.2 9 nan Morphological trait Root RM215 RM205
Osa09LNT0450200.2 9 Spk(t) Morphological trait Culm/leaf nan nan
Osa09LNT0450200.2 9 nan Morphological trait Root RG667 RZ404
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