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

>Osa05LNT0311900.3

CCCCGCCGCCGCACCGCACACCATCCAGGTCCCCGCCGCCGTGCTGCCCCATCCAGCCCCACATCACCACACCACGCCCCCATCCAAGCCGAGTCCGCCGTGGGCACATCCCCATCGAGGGGGCCTCACCTTCATCCCCACCTGTGACGGCCGCCTCCATCCACTGCTCCGGGAGGAACGCTACACATGAAGTCGGAGCTCCGTCTGTTAACCCCGCCTGCTCCTCCTAGGCTAGGACGCCACTGTGGCTGAGGCAGACGACTCTACTCGGCCCTATCTACATCAACGTGCTTCGTAAACGAGAGACTATATACGATATGCTAATGGTAAGGGGACCGGGTTATAGCAGAATGGAGGGTGGAGCAGCTAGATTCTTTCCAGTCTGAAACCGGTAATTACTGCACGGCTTGAGATCATCTTGTACCTGGTGGCGCATGCAGATGGTGCAGCATTGCTGCATGGAGGATCTTTGGATTTTTATTTTTTTCCCTTCAGTTCTTAGTTTTCTGCTCCTGCTTCTATCTGTGCTGTCAAATTGCTTTCTAAAGAATACATTTCAGCACTAAGATTCACAGGTAGTTGGTTCCATGACAGAGTATCCTAACACATCCTATTCTCCCCTATCGGTTTTTATAACCAATTATGCCTCTTCTACACTGTAATGAGTGGTAGACCATAAATTAAAGATCTGAGTTAAGACTGAAGATTGCTAACACCCTAATCAAAATGGAGGAGATGTTCTGTTAATTGTTGCTTGCATCTTCTTCTATCGGTTGTGTTTTTTACAGATTGTGTGAATTGAAAATCTAATTCAGTTTTTGCTAGAGTGAATAAGATTTCATATTTTCCTTACGAGAGAGAGGATAAGATTCAGTTTGTTCCAAAATATATTAATCTCCTGGCAATGCAACACAAAATGACAATCATTTCTTCAAGTGCATAATATTCTAATGTTCTTTTTGTAGAACATTATTATTAACTATTTGTGATATCATGCATGAACTCCAGTACACGACCACCTCAATTTTTTCATCCTCTGCAACTGTGACCAGCTGTGTACTGGAGAGGCTGCAGAATATCATGGAAGCAGTACATGGAGCTGATTGCACCAAGCACTCTGCCATGGTCATGATCAGGACGAGATGTAGGGCTAGCGACAGAGCATGGATGCAAATTATTGCTCTATCCCAACAATTGGTTGGATCTCCCACTTGATTGAAGGTATCATGGCAAAGGACTGGGATTGATTTGTGTTGTCAATGCACACATTTGGTTAGTCAGCCACTAAGATGTGTCTATTGCCTCCCTGGCAGAGTTTGTAAGAACTGAGGCTCATTCCGTTTCTATTGAGTCATGTGTAGCTAGCTAGTATGTAGATCCATTCATGTTGTGTTCTTGCCTCATGATGTTCTTAATAATACCAGAGAATCTACAGCTTATTATGTTCACATGATATTTTTGTATG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.24679
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa05LNT0311900.3 5 21613858 A G
Osa05LNT0311900.3 5 21613953 C T
Osa05LNT0311900.3 5 21615240 T G
Osa05LNT0311900.3 5 21615777 C T
Osa05LNT0311900.3 5 21616007 C G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa05LNT0311900.3 osa-miR6247 Cleavage 3.0 14.831 1 21
Osa05LNT0311900.3 osa-miR159a.2 Translation 5.0 18.831 1 21
Osa05LNT0311900.3 osa-miR319a-5p Translation 5.0 20.889 1 21
Osa05LNT0311900.3 osa-miR438 Cleavage 5.0 13.053 1 21
Osa05LNT0311900.3 osa-miR1439 Cleavage 3.5 14.143 1 21
Osa05LNT0311900.3 osa-miR1862c Cleavage 4.0 10.997 1 24
Osa05LNT0311900.3 osa-miR1862e Translation 5.0 13.63 1 24
Osa05LNT0311900.3 osa-miR2872 Cleavage 4.5 15.093 1 21
Osa05LNT0311900.3 osa-miR1863b Translation 5.0 17.755 1 24
Osa05LNT0311900.3 osa-miR1862f Cleavage 4.0 10.997 1 20
Osa05LNT0311900.3 osa-miR1862g Cleavage 4.0 10.997 1 20
Osa05LNT0311900.3 osa-miR2863c Translation 4.5 14.449 1 24
Osa05LNT0311900.3 osa-miR5340 Cleavage 5.0 16.355 1 23
Osa05LNT0311900.3 osa-miR2275c Cleavage 3.0 12.004 1 23
Osa05LNT0311900.3 osa-miR5823 Cleavage 5.0 14.151 1 24
Osa05LNT0311900.3 osa-miR1862a Cleavage 4.0 10.997 1 24
Osa05LNT0311900.3 osa-miR1862b Cleavage 4.0 10.997 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa05LNT0311900.3 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0311900.3 5 nan Physiological trait Eating quality RM305 RM178
Osa05LNT0311900.3 5 nan Morphological trait Seed RG13 RG573
Osa05LNT0311900.3 5 qNBL-5 Resistance or Tolerance Blast resistance RZ649 RZ225
Osa05LNT0311900.3 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0311900.3 5 nan Morphological trait Seed RM163 RM31
Osa05LNT0311900.3 5 nan Physiological trait Eating quality RM163 RM31
Osa05LNT0311900.3 5 QPl5 Morphological trait Panicle/flower RG13 RG346
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