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

>Osa04LNT0279100.1

CAAAGCTTTATGGATAAATCAATAAAAATGGGCCTCAATAATGACTTCTCCCCTAGTTATACAATAAGCTTCATGTACATGACAGAATCTGCAGCTAGAAATCAAGAGAAATAGGCTAGCAAAAAACAAGGTGAACCTAAAGAAATTTGTATTCAGGAGTGGCAATGGCCTGACCGTGGAGATCTGAACCACCCTAATGCTGCGGCGTATGCCTTCTCCTCTCCCTATTCCTATACCAGCTATTGTTAATAAATCTGCTGTTCTCTTCCAATTTACAAAGATTCCTGTAACAGAATATCTCCTATATATCCACTAGTATGGAGGAATTTTTTTAGTGTAGGGTACCCATGCAACTCTGCAGAACTCAAAAACGGGTGTAATTTGAGAATGAGTTCATGAGGCGGTTTATGGATTCAGGGTAGAACTTTCTCGCAAACAAGTAACACGGTCTCTTCACTCCATTCCATAAGCAAGGCCTCTGCGTAACCACTTTCTTGCTATCGCTGGTGATATGGTAGCTCATGTCAATTGATGTTATATTCTTCAGAAGCTCGTATGTAACATCATTTGCCCGATAAGCTTTCGGATGCCACTTCCCTTCAGACCAGTCAACATGAGTCACAGACCAGTTGGCAATTCCATTTGGATCTATCATATGGAATAGTGTTGGCAAATAATGCTCGTCAGCATAGCAGTTGCGACCATCTTCCATCCCAGGCTTACAATGAAGCTTGAACTTAGTATAGTAAAGACTGTCCGCAATTATCATCAATGCATGCTGACGCTTGACTGAGAACCACTGTGAACCCTTCCTGAAGTCACTCTCTCTAACTTCAGGTAACATATGTTTAGAATATCTAAAATTTCCATGTGGTCCAGGATCATAAAAGGAATCAATAAAACTGATATTTGTTCCTATCAGGTAGTTATACACATAATCAAAATTGTGCAAAGGTACACAGCTGTCAGAGAGTAACACAAAATGCTGATTGTCAACGTCTTCCAGTGCATTTGCCAACAACCTTCTCTCTGCATCAACCATGGAAATCTTACCCCATACCACCTTTTCACTGCGTATGTCTCGATCAATAAATAAGGGACTGGCATGTTCTGGTTTCTCCCTTGAGGCATGAACATATATGGTATATCTTCCCTCATGACCCTCAAAAAATTTCTCCCATAATCTTTCAAATGGCAATGTACCAGGAGTTAAGAACATGAAAGCAACTTTTGATCTCTTCGACTTAACAGGAGGTGTTGATAGGATCTGTTTGAAAACAACTTGTGAGGCTCTCTCTTGATCCGTCAATTCCCTGACAGGCTCTGCAGGTAACCAATCTCTCATAGGAGACGTATAATGCTGGGGTGGATAGAGATAAGCCCACAGTGTTACAATGGAGACGAAAGCTACAACAAGTATGCACAAATGTTTTTTCGGAGAAGTTCGTCCGCGAGGGAGAGGAGCAGACTTCATATCCTTGATAGGTAACTGCCACAATTGGTGTGCCTTCATCTATTAAATCTTCACTGTGAAGGCTTGACTCCCATTACCCTAAGATTTTACCAGCTTTTCCTTCAGCTCGAATTCGAACCGAGATGGGAGGGCCGCCGGGGCAGCGGCGCAGGATCGGACGCCGCACGCCGCGCGGGCGGAGGAGATCCCAGAACCCGCGACCAAAAGGATGGGAATCGAAATCGAACCGAACCGAATCGGATCAAACGGAAAAAAAGGCGAATCGCTCGGTGAATCCGCCGCGAGATCCACACAAGCCCCTTCCCCCCAACAAGCCGACGCCGATCAAAGCTAGCTACAATGGCGCGCAGCTTAGCTCGGGCTCGGCGCGAGAGAGGAGTCGGAAACCGATCGCGAATCTGCCGGGGAGGGTTTATATCGAACGCGGCAACGCTGCCCCGCCCCTGCGACCGCGAC

Coding Potentia
Explanation CPC Score
noncoding -1.26234
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0279100.1 4 30692792 C T
Osa04LNT0279100.1 4 30692843 G A
Osa04LNT0279100.1 4 30693857 A T
Osa04LNT0279100.1 4 30693972 T C
Osa04LNT0279100.1 4 30695633 A T
Osa04LNT0279100.1 4 30695681 A G
Osa04LNT0279100.1 4 30696061 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0279100.1 osa-miR408-5p Translation 5.0 18.419 1 21
Osa04LNT0279100.1 osa-miR5077 Cleavage 4.0 15.09 1 19
Osa04LNT0279100.1 osa-miR5154 Cleavage 5.0 21.098 1 24
Osa04LNT0279100.1 osa-miR5519 Cleavage 5.0 14.994 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0279100.1 4 nan Morphological trait Panicle/flower RM303 RM348
Osa04LNT0279100.1 4 nan Morphological trait Panicle/flower RM303 RM255
Osa04LNT0279100.1 4 qPN-4b Resistance or Tolerance Drought tolerance RM317 RM255
Osa04LNT0279100.1 4 Xa2 Resistance or Tolerance Bacterial blight resistance RM317 RM349
Osa04LNT0279100.1 4 nan Morphological trait Root RM3288 RM5503
Osa04LNT0279100.1 4 pss4.1 Physiological trait Source activity RZ740 RZ590
Osa04LNT0279100.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0279100.1 4 OsAOX1a Resistance or Tolerance Cold tolerance R2737 R740
Osa04LNT0279100.1 4 rfw4a Resistance or Tolerance Drought tolerance RM349 RM1136
Osa04LNT0279100.1 4 nan Morphological trait Root RZ23 RM255
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