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

>Osa04LNT0280800.2

CTACTTTGTTAGCCCTTCATCTGCGTGGTGTGTACTGTGAAAAGGGCACACCCTCTTGCGCATTGGAGGAGAAAAAGGGAAACAAAAGAACAAGGCCAAAGGGAAGGAAATTAAGCAAGCAAAGCGCACGAGGCACGCTCATGAACTCACACCACCTAGGTCAACCCAACAACACGGCTCGACCAAATTCCAGCGAGGAAGCGATGCCCAAACACCTGTAACACCATGTGATCCCGTGCGTGATGCACGGGCATACCAGACTGCTACTACTTCGTTCCAAAATATTGTACCTAGAATGTGATTTGACCGATCCTAAAGATAACGAATCTAGACAATCTCTATTTCGATTCATTATCTTAGGATGAGTTAAATCACATTCTAAATTACAGTATTTTAGAACGGATTGGAGGCAGTAGATGCCTTAGATCGTTCAATCACCTACTCCCTCTTCCTCCTACCCAAGTCAGCAAGTGATGAGACCGCCTTTGTATGAGCCGGGAATTTAGCTCCAAGCCTTCCTTGCCCTGCTTCTCGGTTATCTTCACCTGCCCTCGTCGATGATGGAGGTGAACAATGGCGAGGGAGTCAGCGGGCTGCCTTCCCCTGCGCCCTGGCTACTCGCCTGGCCGGCGCCGCCATCACCGGAGGACGGCGGCGTCGACGCCGAGCCGACCTGGCTGCTGCCCGTGTGGTGGCAGCTCCCGACCTTGATCTGCCACTCCGTGATGTAGCTCGGCTTTGCGGCATCTTCGGTTATGTCGGCGTCTCCGGTGAGCATGGAGACTACCTTCGACATTGGCGGCCGCTTGTGAGGGGAGCCCTGTGTGCAGAGGAGGGCGACGCGGATGACTCTGATCACCTCCTCGCTGTTGAATTCCGAGAGTTTTGGGTCCACGAAGTCGAGCGGGTGCCCGTTTTCATACAGCTCCCAGACCCTTTCAAATATGTAAGTTCTGTCTTCCTCAAGTGTATTCTGGTAGTTTGATTCACCAGCAACAGTCTCCAACGCGACCACGCCGAATGCAAACACATCAACTTTCTCAGTCATATGACCTCTCATGGCATACTCAGGTGCAAGGTAGCCAAATGTGCCAGCAACTTTTGTGCTGACGTGAGTTTTCTTGTTATCATAGAGCTTGGCAAGCCCAAAATCTGAAATCTTAGGGTTGAGACCGGCATCTAGCAAGACATTACTGGCCTTTATGTCCCTGTGCACGATGCGGACGGTAGAATCCTCGTGAAGATAAGCTATACCTCTTGCTAGGCCTAAGCATATCTCAAATCTTGTTGGCCAATCCAGGTTCAAGCTTCCCTTTCCAAACAGTGCTTGGTCAAGGCTTCCATTCTCCAGATACTCATAAACCAACAGCGGCGTATTGCTCTCAAGGCAGCAACCATACAATGTCACGAGGTTACAGTGTTGTACTCGAGATATAGTTTCGATTTCTGTAGCAAATTGCTTTTTCCCCTGATTAGATGACTGAGAGAGCTGCTTCACTGCCACCGCCCTTCCATCACTTAATCTACCCTTGTGAACCAATCCATATCCTCCTTCACCAAGTAGGTTACTAGAACTAAAATTTTCCGTAGCTGACCTTAGCTCATTATAACTGAAGACATTTGGTCTTCCAACTATGTTGTACAGCTCTTCTAGCTCCAATAATATCTTTCTCTTCTTCTGTCTCCATATAAAGTGTCCAGCAAGTGCAGCCAATGCAAAAACTGCAACACCAACCATAACTACAATGATCACAGCAATTTTGCTCCTGCTCTTGTTGTCTGCAGGGCTACGGACCGTTGGGATGAAGTTTGGAGTAGCGCTCAAAGCTGATATTGCAGGCCCATAGTAGCCTTGATGAGGAATGCAGCAAGTACCCTTGCCAGCCCAGAAGAGATGAATCTCAAGGAAATTTTTTGTCACAGGGACAACATACTGCTTCTTAACAACAGTGAAAGATTTCCCTCCTGCTGCCTTTCTTATGTCAAAGTTCTGCTCCTTACGCTCCCCCTGAATGTAGATGTCAAAAATCCTCCTCCCTCTGCTCCTCCAAGACTGCACATCAGGGAAATCCACCTCGGCAAATTGAAGTGTTACAGTGTAGTTCCCATTCTCGAGTCCAATGCCATAGTATCTCAAAGATGATGGTGACATCCTTGCTGTTTGGAACAGTCCAGAATCTAGTGTTTTATCGAACTGGCGTGAACTGTAGATTATGTAACTTCCATTGGGTGGATCCATGAATCTTCCAGTGGTGCTAACACCCCACGTAGGTGTGCCTGCCACATAGTATGATGCAGCACCAAGATTGGCGTTATCAGCCTGATACATGGCATTATCTGAGCCTGATATGGTTCTACTACCACCACAGTCCACCGCGAAAGAGGCAGACTTCGGAGAACCGAGAAAACAGGGGGTATTCCGCTGAAGACAATTCAATCCCCATGGCAGACCACTCATATCAGTGCCATCAATCACAAAGTCATTTGCCACCAAATTCAGTTGTAAATCTTTCTGGGCAGTCCAAGAAGGAAAGTTTCCTGAGAGGTGGTTGTATGAAAAATCTAAATTTGAAAGCAGAGGACTTTTCATGGCTGGCAGACTTCCTGAAAGGCTATTATTCCCAAGAAATAGAAAAGTAAGAGAAGGAAGATTCACGATTGACGGAGGAATTTGACCTGTGATATTGTTAAAACTCAAATCCAGTAGATTTAAACTTCCAAACTTGGAGAAGTCCACTGATGCAAGTGAATCAGAAATCCTGCTGTTTCTCAAGACAAGATCACCCAAAGATGTCATGCTTCCAATGAACGCCAGTGAAGAGCTTCCATTTACTATATCCCCTATTCTTAAGCTTCTCAACTTGACAAGATTATATAAGCTTCTAGGAATAGGACCTTGAAAAGAGTTCCCTTGGAGCCTCAGTTGGGTTAAGTTGGTCAAACTCCCAAGATAATCAGGTATTTGCCCAGTGAAATTATTATCCAATGCCCACCTGGATGCACAATGACAATGGTGTCCATAATTATTTGTTGAAATTTCATGAGAAACAATAAAATCCCAAACACTGCTTTGCGAAATTATAAGGTGGACAGGTTCGTAAGTTGTGATAAAGTCGTTGGTAGAGGACCACTGAAGTCGTTACTATCAATGTACAGCTGTTGAAGTTTTGTCAATTTACCCAGCTCATCGGGAAGTGATCCATTAAAATTATTTGAGCCCAATGCCAGCGATACAAGATTTGTAAGATTGCCAAGCTCCTTGGGGATAGGTCCAGACAACGCATTGATGCCCACAGTAATGTACTTGAGAGCAGTCAGTTCTCCGATGAACGCTGGTAATGGCCCGGTGAAATAATTCTTCCTGAAGTCCAGCTTGATGAGGTGAGTGAGGTTCCTGAGCTCTTCTGGGATCGGGCCGACCACATCCAGCGTGTTGATTTTCAGTCTGGTGATGTGGCAGAGCGTGTTGTTGTGATCGGAGCAGTCGCACTTGATGGCCGGGTTGAAGGCCGGGTTGTCGTCCAGCGGCGTGTCGTCCGTCGCGGCGCCGCTGCACGGGTCGCTGCTGATGTTCCACGACGGCGGCGCGCTCAGCCCCAGCCTCGCCATCATCGCGTTCAGCGCCGCCGCTTCGGTTGGATCAGTGTGAGGTGGTGGTTGCTGAGCCTGAGCATCTGCTGCTCTCCAAGAACACAGCAGCAGCACAAGCACGCAGAGACAGCCATGGAGGTAGCAACAGTAGCTCAACCTAGGATCCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.912106
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0280800.2 4 31265374 A C
Osa04LNT0280800.2 4 31264187 A G
Osa04LNT0280800.2 4 31263968 A G
Osa04LNT0280800.2 4 31264009 A G
Osa04LNT0280800.2 4 31264667 C T
Osa04LNT0280800.2 4 31265163 A G
Osa04LNT0280800.2 4 31266259 T C
Osa04LNT0280800.2 4 31266804 C T
Osa04LNT0280800.2 4 31266860 T C
Osa04LNT0280800.2 4 31266869 A G
Osa04LNT0280800.2 4 31266888 T C
Osa04LNT0280800.2 4 31267121 G T
Osa04LNT0280800.2 4 31267995 C G
Osa04LNT0280800.2 4 31268122 G T
Osa04LNT0280800.2 4 31268322 G A
Osa04LNT0280800.2 4 31269521 A G
Osa04LNT0280800.2 4 31269816 T C
Osa04LNT0280800.2 4 31270029 C A
Osa04LNT0280800.2 4 31270090 T A
Osa04LNT0280800.2 4 31270123 G A
Osa04LNT0280800.2 4 31270272 G A
Osa04LNT0280800.2 4 31270291 A G
Osa04LNT0280800.2 4 31270302 T C
Osa04LNT0280800.2 4 31270373 A G
Osa04LNT0280800.2 4 31270418 C T
Osa04LNT0280800.2 4 31270450 G A
Osa04LNT0280800.2 4 31270391 A G
Osa04LNT0280800.2 4 31263556 A G
Osa04LNT0280800.2 4 31264248 C T
Osa04LNT0280800.2 4 31266889 A 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
Osa04LNT0280800.2 osa-miR5788 Cleavage 4.5 18.449 1 21
Osa04LNT0280800.2 osa-miR5795 Translation 3.5 16.647 1 22
Osa04LNT0280800.2 osa-miR6254 Translation 5.0 22.207 1 21
Osa04LNT0280800.2 osa-miR6256 Translation 4.5 11.298 1 22
Osa04LNT0280800.2 osa-miR156a Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156b-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156c-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156d Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156e Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156f-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156g-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156h-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156i Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR156j-5p Cleavage 4.0 14.155 1 20
Osa04LNT0280800.2 osa-miR164e Cleavage 5.0 20.597 1 21
Osa04LNT0280800.2 osa-miR535-5p Cleavage 5.0 18.388 1 21
Osa04LNT0280800.2 osa-miR1428a-3p Translation 4.5 18.125 1 21
Osa04LNT0280800.2 osa-miR1439 Cleavage 2.5 17.942 1 21
Osa04LNT0280800.2 osa-miR1428b Cleavage 3.0 18.125 1 21
Osa04LNT0280800.2 osa-miR1428c Cleavage 3.0 18.125 1 21
Osa04LNT0280800.2 osa-miR1428d Cleavage 3.0 18.125 1 21
Osa04LNT0280800.2 osa-miR1428e-3p Cleavage 3.0 18.125 1 21
Osa04LNT0280800.2 osa-miR1858a Translation 4.5 16.147 1 21
Osa04LNT0280800.2 osa-miR1882a Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882b Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882c Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882d Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882e-5p Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882f Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882g Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR1882h Cleavage 4.0 14.117 1 24
Osa04LNT0280800.2 osa-miR2101-3p Cleavage 5.0 17.656 1 22
Osa04LNT0280800.2 osa-miR2873a Cleavage 4.5 11.528 1 24
Osa04LNT0280800.2 osa-miR2873a Translation 5.0 15.186 1 24
Osa04LNT0280800.2 osa-miR2873a Translation 5.0 19.308 1 24
Osa04LNT0280800.2 osa-miR2920 Translation 5.0 10.143 1 23
Osa04LNT0280800.2 osa-miR2873b Cleavage 3.5 11.843 1 21
Osa04LNT0280800.2 osa-miR2873b Cleavage 4.5 13.895 1 21
Osa04LNT0280800.2 osa-miR5160 Translation 4.5 15.368 1 22
Osa04LNT0280800.2 osa-miR5492 Translation 5.0 6.276 1 21
Osa04LNT0280800.2 osa-miR5498 Cleavage 4.5 16.174 1 21
Osa04LNT0280800.2 osa-miR5506 Cleavage 5.0 13.361 1 21
Osa04LNT0280800.2 osa-miR1858b Translation 4.5 16.147 1 21
Osa04LNT0280800.2 osa-miR2094-5p Translation 4.5 18.242 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0280800.2 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0280800.2 4 nan Morphological trait Root RM3276 RM3335
Osa04LNT0280800.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0280800.2 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0280800.2 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0280800.2 4 nan Morphological trait Root RZ23 RM255
Osa04LNT0280800.2 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0280800.2 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0280800.2 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0280800.2 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
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