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

>Osa03LNT0231500.1

GGAATTAATATATGCTTAGGCTATTTAAGACTTTTACAGCCGCAGTACCCCTCAATTCCCCCAAATTGTCGTGTCGTGGAACGTTTGTGCTTGCACGAGTGCACGGTACAGGTACAGTGCAGGACCATGCTGCACAGAGAGGACATCACGCGTGCTAATCCATTGCAAATTATTGGATTTCATCAATTTATTGTAATAAATTATTAGTCAAAGGCAAAGACTGCATCTTGGAGTGAGCTGACGTCAAAAACCATATTTCATGCGGCTTTATCTCACAAAACAGTGAGGACACCCTGAAACTCCTGCCTCTTAAGAAGCTCTTTGGCAATCCTGCGGCCTCTTTCCTCCAACCAATCAACCGTCGGGAGACCCTTAATTCTAACCATCGGATCCATGATCATACAGTCAAGTCTACTAGCACAACGACGAATGTGGTGTGCTAGCTCGATCAGCCCCTGCCAATGACAGGCTCCAGACATGACCACCCTCTTGAGCTTGTCATGCCGATACGGTAGCATATCCACTCTGATCGCCTGTCTGATGACGAAATCAGAGAAGCGAAAGTGCAGTTCCAGTTCCTCTAGAACTGGAGCGAGCTCCAAGAGGTAGGCCAAACGAAGAATCCCACCAACTGACCTGCCGTCCCCATAAAGAGGCAAATACAAGCTCAGATGCCTCAAATTGATGAATCTCACTGAGGTTTTGGCAAAACTTTGCAACTCATCGTAGATGCAGAGTGTCGAGGTAATGGAGAGTTTCTGCACATGCGGAAGAGCGGCAGGAAGCTCGGTGCAGATGTAGTCCAGATTATCACCATAAAGCACGCTCTTATGTAGCAGTTTAATGTTTGCCTCCATCACCTTCAGAGATTCACTTAGTGCCAACGGAATTGGCCGATTGGTCAAATCGACCGATGTGAGGTTTGGAGCTTCCAGCTCAACCTTTTCCATGTAGCAGTAGTGCAAAGAAAGATAACGCAGACGGCGCAGTGGCTTGCACAAGGTTAGCTCAGTGAAGGAAGAGCAGCTGATGCTCAGCCACTCAAGAGCAGTGCACTCCGACAGCATCAGATGTTGGAAGTCATTTAAAAAGGAAACTTTGTGCAGGGTGAGCTTCTTGAGGTTTGCAAAGCCAGTGAAACCAGTGGTTGCTGTGTTCAACCAGACGTAGCTCAGATGAAGGGATTTGATATGAGCAGGGGAGCGGTCAGGGACACTGAAAACATGCAGGTGGAAGATGTACTTTTCATCAGCTAAGCCCCTGAAAATACCCTTCACTCCAGGAGTGAAATCAAAAGTGATGTGCCTTGCTCTCAACTTGGAGCAGAAGCCAACCCATCTGTTGACATGGCAGGTATGTTTCCTGCGCAGCCCAAACTTAACAACAAACTTATTCAGGGTAGGAGGTGCACATAGCTGCCGCAAAAGACTGTTGACTCTCCTGGCAAAGTTGGTCCTTGTACGTCTTATGGTTTTATTCCCAGGCTTGAACATGGTGGCCCTGGTGAAGATCAATTTCGGGCAGCAGCTTCTCCACAGTTTCTGCCACTTGCGAGAAAGAAGGCCCATCCGTGAGGACTCTCTGAATGTTAATCGAGACAGTATGCGGTGCAGGACATCATCGGGCAGATGGTGAAGTTGCAGGGCTTCTGGCTTGGTCATGGGAACAGATTTATCAGCACTTTCTTTGCGCTGCTGGGGATGCTTGACTGCTTGAGACGATGTCAGTTGTGGACGGCGGCACCCTCGGCCTCCACTGCCCCTGCCCGAATCTCAAAGCTTGGGAGGTGAGGCTGGGCAAGACCTGGTTACCACTGCCCGAGACTTCTAACTGCCTGAAATAAGGTGTACCATCAGAACAGTAAGAAAAAATTTGCATGGATTCAAAACCTCAAGCTTCTTTTCATCATCTTAATTGCATAGGATGTTGAGCAGCAGTGACCTGGAGCAGATGCTACGAGAAAATGTAAGCTCGATTTGGCATGCTGTACTTCTCCGCCAGGAAGCCAACGACGATGCAAGGACCCGGGCAGCGTAGAGGGGATGTTAGAGACGCGGCGGCAGTGAGTCCCCACGCGCCGGCGGGGCAGGGAAGGCCACCTCCGCAGATCGGCCTCAGCCCTCAGCGGCAGTGAGAGGGTTTCACCGATGGTGTGGGGAGGGGGAAGGAGCGGCGGCGGGACTGAGGGGGCGGTGGCGGCGCGGGACGGATCTGCGTGAGTCTAGGGTTTCGTCGGTAGTGGTAGTGGTGGCGGTGGCGGTGGCGGCGGGACTGAGGGGGCGGGGGCGGTGGCGGCGCGAGTCGTGGCGGGAGGGAAAGGAGCGTAGGGGAGACGGTCGTGAGGAGGGAGGGGCGCGCGC

Coding Potentia
Explanation CPC Score
noncoding -1.00158
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0231500.1 3 29329304 C T
Osa03LNT0231500.1 3 29332779 G A
Osa03LNT0231500.1 3 29334325 C T
Osa03LNT0231500.1 3 29334952 A T
Osa03LNT0231500.1 3 29335686 A G
Osa03LNT0231500.1 3 29333965 G C
Osa03LNT0231500.1 3 29333947 A G
Osa03LNT0231500.1 3 29330436 A G
Osa03LNT0231500.1 3 29330506 G A
Osa03LNT0231500.1 3 29333803 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0231500.1 DTM_#DNAt_MULE_japo_Os2081 Chr3 - 29330068 29330756 688
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0231500.1 osa-miR5543 Cleavage 4.5 19.234 1 21
Osa03LNT0231500.1 osa-miR5814 Cleavage 5.0 24.036 1 24
Osa03LNT0231500.1 osa-miR5820 Cleavage 4.5 18.253 1 21
Osa03LNT0231500.1 osa-miR531c Cleavage 5.0 18.784 1 24
Osa03LNT0231500.1 osa-miR413 Cleavage 4.0 21.907 1 21
Osa03LNT0231500.1 osa-miR531a Cleavage 5.0 18.784 1 24
Osa03LNT0231500.1 osa-miR1853-5p Translation 4.0 21.808 1 24
Osa03LNT0231500.1 osa-miR2095-5p Translation 4.5 8.769 1 22
Osa03LNT0231500.1 osa-miR2118d Translation 4.0 21.237 1 22
Osa03LNT0231500.1 osa-miR2924 Translation 5.0 23.063 1 21
Osa03LNT0231500.1 osa-miR2924 Translation 5.0 19.228 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0231500.1 3 nan Resistance or Tolerance Drought tolerance C746 RZ448
Osa03LNT0231500.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0231500.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0231500.1 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0231500.1 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0231500.1 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
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