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

>Osa01LNT0046200.2

CGGAGACATGCAAGACGCCCAATGACACGATATAATGACATTTTTTTCTGATCTTTTAGATCAACTTATGAGTTGTAGCAAATACACGATACCATAATATGGGTTCTACATCTATATAGGAACAACAAGAACGAAAAGGGCTGCCCCGTTCGCAAAAAAACATTTATGTACAACGAGAGGGGTCAGCTACAGCGATCAACGAATACTTCTAATAAGGTTACACAAGAGCTCCTGGATGAGGCTGTCGCGAACAATCTGTCAGTCAGCAACTTCTTTCCTTTAAAGAACACAAGCATCCCACTTTTGCCCGTAGATGCTCATACATTTATTGTGCTTCCATTTGCTAGCAATCCTCAAGTTAGATACTAATTAATACCAAGCTGTATGTGAAATGTCCTAGAACATGTAATTTCCCTTTTCCCTTGCACTGATGAGGAGGCATGATGCTTAGAAACGGGGCACTTTTGACAGAGGCCCCATTGTGGGCATTGGTGAAGGCTCAGTAACCGGAGGTCTTGTTTGATGGTTGGCAACTGAATTGTTAATTACCAATTTATTTCCTGTGCTTCTAATACCAGCAGCATCACATTCTGGTTGTTGAGGGTCCACTGATACCTTTACAGGATGTCTTTGCGGATTCTTGTCCTCCCTTAAGAAACCAGGAACAGATAAGTGCCAATTTTTTTCTAGGTGCAGCAATACATCCTTGGCTTCCAGGACTGATGATTTCCTATGCTTCGCAAGGGTACACGCAAATGCAGTCACCGAATCAATGAAGTCATCAGCAATCTCCAAAAGCAAATCTTCCACTTCTGGATCAACCTTGCCCAGGGGATCTACCTGTGAAACCAAATCTTGTATTTTTCTCTTCCCAAGAAGTTGATTAGTTACTTCTGCTCCTTGACTTGCACTTCCACCAGTCATAGTTCCACCTGATAAAGGAGTGCCCGGTTGTGATCCTGTCAGGTTCATGGACTTCTGGGAACCAGATGCTGATATCCTTGGAGATTGTTGTTGTTGCTGAAGTTGCTGTAGAATGTGTTGCTGCTGTAAAAGCTGGGTATTGAGATGAGGATGCTGTTGTTGGGTTTGTGCGATTTGGTGTTGATTCAATCCTGACTGCTGTTGAAGTTGATGTATTAATAGCATCCTTTGTTGATGCTGAAATTGTTGTGGAGAAACAGGTGATCCCAGCGATGATTGCATTTGTTTTAACCATGCTGCCTGCTGCTGTTTCTGAGGAAGGGACATTTGTGCCATCGGCCCATTTGTCGACGATCCAGGTAGCTGTGGATTTAATGCAGCAATCGATGCTGTTCTTGTCAAGCCTTGACCCACAACCTTCTGTGGAGACAGTGTGCCTTGCTGTGATGTCTGCTGCGGCCTCAATTGTGCTTGTGCATGGGCAAAACGTTGCTGATTATATGGAATAGTTCCATTTCCTCTCATACCACCCATGACTCCCATGGACTGCATACCTTGTAATGCTTGAGCTGCATTGGCAGTATTAAATTGTGCACCTTGCACCATACCCTTCTGCCTTGGCTGCAGCAACAAGAAAAACCAATTATGCTAGTAATACAATCAGATGGTGATAGTTACTAGTTACCTTCAACTGAATTATTTTCCCCAATAATAATAATTTCTTAACATAGGCAAAACTAGTACGAATCACTCCTCTTAATGTGGTTTCCAATAAAAAAAAGCAGAGGGTGTTTCATTAAGCAATTCTAAATATAATACAGATATTCGAACAATTGTGGTTGCGCCTGCAAAGATTCCAACAACAGAAGGCTTCTTATCAGAGCTTATATTTGATTCTAAAAGAAATCACAAATATTTTACCAATGGAACATAGTACGAGAAATGTAGATTTCTAGTTTTTCTTTCTTGTGGTATGCACCATCACACCCAAGGAGTTATCTCCACTACTTAAATACCATGATGCTACAAGAAAAAAAAGTCAAAACTGTTTAAGAAATTTCAAGATTCTGGATCCACGATTCA

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.423763
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0046200.2 1 36385730 C T
Osa01LNT0046200.2 1 36388719 C A
Osa01LNT0046200.2 1 36388603 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
Osa01LNT0046200.2 osa-miR5796 Cleavage 5.0 14.245 1 21
Osa01LNT0046200.2 osa-miR812v Cleavage 5.0 13.785 1 24
Osa01LNT0046200.2 osa-miR5823 Translation 4.0 14.351 1 24
Osa01LNT0046200.2 osa-miR5516b Cleavage 4.5 21.322 1 21
Osa01LNT0046200.2 osa-miR6251 Translation 4.0 12.158 1 21
Osa01LNT0046200.2 osa-miR169a Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169b Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169c Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169d Cleavage 3.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169e Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169f.1 Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169g Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169h Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169i-5p.1 Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169j Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169k Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169l Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR169m Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR816 Cleavage 4.0 11.838 1 20
Osa01LNT0046200.2 osa-miR1428a-5p Translation 4.0 17.356 1 21
Osa01LNT0046200.2 osa-miR169r-5p Cleavage 4.0 21.474 1 21
Osa01LNT0046200.2 osa-miR1862d Cleavage 4.0 11.05 1 24
Osa01LNT0046200.2 osa-miR1862e Cleavage 4.5 10.99 1 24
Osa01LNT0046200.2 osa-miR1881 Cleavage 3.5 10.308 1 24
Osa01LNT0046200.2 osa-miR2870 Translation 5.0 24.778 1 21
Osa01LNT0046200.2 osa-miR3979-3p Cleavage 4.5 9.881 1 20
Osa01LNT0046200.2 osa-miR5516a Cleavage 4.5 21.322 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0046200.2 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0046200.2 1 nan Resistance or Tolerance Drought tolerance RG690 RG810
Osa01LNT0046200.2 1 yd1 Morphological trait Seed C2340 C86
Osa01LNT0046200.2 1 yd1b Morphological trait Seed C547 C2340
Osa01LNT0046200.2 1 qNSB1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0046200.2 1 qSSBp1-1 Morphological trait Panicle/flower C86 C2340
Osa01LNT0046200.2 1 qChll1a Morphological trait Culm/leaf C86 C813
Osa01LNT0046200.2 1 qH2O21 Others Others C86 C813
Osa01LNT0046200.2 1 An10 Morphological trait Panicle/flower nan nan
Osa01LNT0046200.2 1 qLVBTS1-1 Morphological trait Panicle/flower C2340 C86
Osa01LNT0046200.2 1 sf1.1 Physiological trait Sterility RM212 RM315
Osa01LNT0046200.2 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0046200.2 1 nan Resistance or Tolerance Insect resistance RM543 RM472
Osa01LNT0046200.2 1 dth1.1 Physiological trait Flowering RG541 RG109
Osa01LNT0046200.2 1 ng1 Morphological trait Panicle/flower RG374 RG394
Osa01LNT0046200.2 1 nan Physiological trait Source activity RG374 RG690
Osa01LNT0046200.2 1 sf1 Physiological trait Source activity RG374 RG394
Osa01LNT0046200.2 1 ng1 Morphological trait Seed RG374 RG394
Osa01LNT0046200.2 1 sf1 Morphological trait Seed RG374 RG394
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