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

>Osa04LNT0289200.2

TCTCAACTAAGTTATTGCCGGATGTACATGAGCCAAAATTGCACAGGCTGGAAACACAAAAACTAGAGCTGTATTAAAATATCCCAGTGGCTGCCGCCTTGTTCAGCGTTCTTCTAAATTTAGTACACATATTATATGACAAAACAGAAAACTCATACCAATCAGGTGTGAGTAAAAAAATATTATACATGCAAGCATCCGACATATATACAAAATCATTTCTATGCTGCCGTGCTAGCAACAAACAGTAGCCTGGTAGTTTTGAAGAAAACCTCTAAGCTGTTTTCACAAAGGTCACAAGGAGCCCATGTATTCTCTATCGCGCCGATTTCTTTTGTATCTTTGCTTTGGGATGTCGACTTCCTGTCTTGGAAACCAGGACATGCCGTAAGATATCTTCCAATTCTACAGTAATCTCTGAGAAAAGGGGCCGCACATGAGGATTTTCATCCCAACATCGTTCAATCAGTTTGGACAACCTCGGATGCACCTTCGGTGGGATCTCCATGCGCATTCCCTGCCTTACTCCCAGTGCAGCTTGCAAGGGTGTCAGATTTTCGTATGGTATCTTTGTAGTGACCAACTCCCATAGAACAATAGCAAAGCTGAAGACATCTGCCTTATGGTCATAAGGCTTATGGTTTATTACCTCAGGTGCCATCCATCTATACGTGCCAGTTTCAGCAGTCATTTCTCCCCCTTGAGATCGGAGCCGAGAGACACCAAAGTCTGCGATCTTCACGACTTGACCAGAGCCAATTAGCAAATTGGCAGTCTTCAAGTCCCTATGGATGATATTATTCTGGTGCAAATAATCCATTCCTTTTGAGATACCAATAGCAATCCTAAGAACAACAGGAAGCTCCAAAGTATTGTTTTGCTTATGAAGGAAGTCATACAAATTACCTCCGGGCATGTACTCTGTTACAATGAGATACTTTCGATGCTTTGTGCAAGCTCCATAAAATTGGACAACATTTTCATGATCAACACTCTTTAAAATCATTATTTCTTGCAAGAACTCCACTTTCGAAGAATCGTTAACATGTTCAGATCTAAGAAATTTTACTGCAACATCCACACCGAGATAAGTTCCTCGATATAGATCCCCAGAAGATCCGGATGCAATTTTCTCCCCAATTTGCAGCAAACTCCTGTCGAATTCAGAATCTCCTATCTTTTCCTGCAGCTCTAGAACTTTCTCTGATTGTGACAAATTTGTCGGATTAGACAATGAGCCATGGCTGCTTGCCTCTGCCTCTATAAGCTTCTGAAGCAAACCATCCGTTTCCTCTGTATCCCAGCCATCAACAACAAACACATCGAGACAAAAGCCATCTGATGTTGAGAACACATGAGCTTCACGGATGTTCAACCCAATATCAGACAGTATCGCGGATAGCTTACTGAGGAGCTTTGGCTTGTCTATGGAAGAAAAAATAATTTCATGAACACGGACGAATTTCGAGTCCCTTCTTGCAGAACTGGCTTCGAAGTCATCCACACCTTTTCCTCTCTCTAGACTCAGGTCTTCCATCATCCTTTCATATGGCTCGGATTCTGTGAATTCATCATCTCGTTTTCAGTTGGAGTTGATCCAGAGTCTACCCCTATGTAGCGGGCATGGAAGATTGGGCGCTTTTCAGGGTCGGCGCAGTCGGCGAGAATCCTCCGGTGCAGCAGCACTTGCTCTGCCTTGCTGACATCCAGATCGATCAAATAGCTTTCGGGCAAGCGAAGGAAGTGGCGGTCGAGCTCAACGCGGAAGGAGGAAGGGTTGGAGATGGCCTCCTCGTTGCGAATCGCCACCAGGCGCTCGTAGATGACGTTCCTAATGTCAGGGGACCCGTGCACGCTACCGCCGCCGCCGCCGCCGCCGGAACCGAGTCCCGCGGCGGCGGCGGCGGCACGGGGAGAGGGTCCCGAGCTCTCGGCCACGCCCTCCTCGATGTCGTCCTCCATCTCCCCCGCGGCGGCGAGGTGCCGCCTACGCGAGTCCCCCCATAGCGACGTCGTCCACTACGTCTCAGGAGGAGGCGGCGAGAGAGATGCGGTAGTAGAAGCAGCCTGAGCTGAGGTATCCAATCCAAGAGGTGGTGAGGAATCCGAGGGGACTCTTTTGGCGCGAGAATCTTCTAGAGGATGGCGCGCGCCGGCCGGCGGGCGGTGGGCTAATATTGTAGGGTGAAATTCCTCGCCGGAGCGGAGATTCCAATCCAAACGCCGGCGAGGCGAAGCGAGACGACGAACTGAGCAGCGTCTCGCTCTCTCGCCAGCTCGCAGGAGGAGGAGGAGGGAGATTTTCCTTTTCTCTTTTTTTTCCTTTCTTTTTATTATGAATTTTTGGCTTTGGTGGAATGGAATTATGGAAAAAAAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.931809
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0289200.2 4 35094022 A G
Osa04LNT0289200.2 4 35091992 A G
Osa04LNT0289200.2 4 35092127 G A
Osa04LNT0289200.2 4 35093963 A G
Osa04LNT0289200.2 4 35094114 A C
Osa04LNT0289200.2 4 35094145 C T
Osa04LNT0289200.2 4 35095761 G A
Osa04LNT0289200.2 4 35098008 G T
Osa04LNT0289200.2 4 35098177 G A
Osa04LNT0289200.2 4 35098298 T 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
Osa04LNT0289200.2 osa-miR5822 Cleavage 5.0 18.127 1 21
Osa04LNT0289200.2 osa-miR166c-5p Cleavage 5.0 22.414 1 20
Osa04LNT0289200.2 osa-miR319a-3p Translation 5.0 12.06 1 21
Osa04LNT0289200.2 osa-miR166k-5p Cleavage 4.0 22.414 1 21
Osa04LNT0289200.2 osa-miR418 Cleavage 5.0 18.679 1 21
Osa04LNT0289200.2 osa-miR444d.3 Translation 5.0 14.222 1 21
Osa04LNT0289200.2 osa-miR1846e Cleavage 4.5 20.975 1 20
Osa04LNT0289200.2 osa-miR2106 Translation 5.0 16.394 1 21
Osa04LNT0289200.2 osa-miR5488 Translation 5.0 20.192 1 21
Osa04LNT0289200.2 osa-miR5503 Cleavage 4.5 15.532 1 22
Osa04LNT0289200.2 osa-miR6252 Translation 5.0 18.06 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0289200.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0289200.2 4 nan Resistance or Tolerance Drought tolerance RG143 RG620
Osa04LNT0289200.2 4 nan Morphological trait Panicle/flower RG620 RG214
Osa04LNT0289200.2 4 Sh(t) Morphological trait Panicle/flower nan nan
Osa04LNT0289200.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0289200.2 4 Sh3 Morphological trait Panicle/flower nan nan
Osa04LNT0289200.2 4 iSh3(t) Morphological trait Panicle/flower nan nan
Osa04LNT0289200.2 4 Sh3-gla 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