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

>Osa01LNT0009400.4

TATATGTATCCCGAAACACAGAGCTACTATTGCGTAAGTAACATCATACTGGGTACAGCAGCAAGCATTCGTGTTTATCGTGTGCTATGCATGATAACATAGAATCCTAGCCACATAATGCGTAGGGTCGCTGTTAAGTCTTTACAAAAGGAAGCGTCTGGCTACAACCATGCTCAAAGGTCTATAGCGAGCGACAAAATAGCACAGTTTGTAAATGCATGGCACAATATTAACCAACGAAACACTGTAGAGTGGTTCTAAAGAAGCTTGGTTAAGGTACCCATGCAAGCAGAGCATGAGACCGATGCCGAGTCTGATACAACTGTGCAAAACAAAAGCGTACACATTCCTTTGCTGCATCAGGCCTTGTTCTCGCCGCTGCCATCAGCGGTATCGTCACCACTTTCTTTGAACAACTTCTTAGCTGTGCCAGTGCCAGGAGATGGCCTTGCCCTTTTGTTGTGGGACTTGGATGTGGTTTTCTTAGTAGCAGAATGACCACCCATTTGGGAAAGGGGCAAATTGTCATCATCCTCATCTTCTTCGTCAAGGACCTGAACTGGAGTCTTGGACTGGCATTCAACATCATCATTTTTGTCCTTGGCTCCAACAACCAACGGACTGTTTAATCCAGCCGATGGAGTGGCAGGCGGATCACTGAATCCAATGGATGGAGCAAATGCTGCTGTGGACTGGCCAACAGAGAGTTCATGTGTTACACTTGGTGATAGAGCTAGAGAAGGTACCATGGAGGATGCCTGAGATGCAGATGGAGATTGTGGGTGGCAGGATTCTGGCTGTTGCCGTTTCCGACAATCATATTCACTTGGAATGAGACATTGCTTGAAGACATGGTATTCTCGGTAATAGCAACTTTCCAGGTGAAATTTTCCTCAAGCAAATTTGTGATCTCCTTGGGTATGGCCTCCTTGCCGGCAGCGTTGCCCTCTAACAGAATCTCCACTGATCGACCAATAAGACACTGTGCTAGGCGGCCAAAGAGCACGAACTTAGCGTCAGCTGTGTCATCACCTGCCACAACGCTAAGCTTGAACCTAGGTGATGCTCCCACAAGAGGAGGGCATGACTCATTCTGGCACTTGTATGCGTTTCCATATGGCCTTGCTGTTCTCCTGCATATATCACATGCAGTGTACCACCAAGAGTACTCCATGTCTATTTTCTTGATGACAACAGTAACCAAGAATTCATGTTTCTGATAAAGAGACATCGCCATAGCCCTTCACAAGGGTGCCAACGAAGATTACTATCTGTGGTTCTTTCTGACCAGCAACAAACACCTCATCGGCAGGAAAGCTTGTTGCACGTTCCCCCCAAAGCGCCACATTCAAGATTGCATTGTCAGTGTTGCGGATGAAGACACTCCTCTTTACGGTGCCTTGAAGCGGAGTCACGGGCGACAGCTGAGTAATAATTCCAATGATATCTGTGAATGAGTCTTTCTTGCCAACACGTGAGCGAAGACCGCCAAATGGTGAGAGTGAATAAGTATACAAAGGAATCTCAGCTGGTGGATCGACACGCTCCTCTAGTTTAGTCCACCTTGTGAAATAGATGGACATGCAGTTGTCGACTGGTTTGTACTGCCTGTTACACTTCCTCACACGGAAGTACTTAATGTAGTACACCTTGCCTTCAGTGATGATTGGCCTGAATATCTCATCACATGGGGGATAAATCTGAGCAGCAATGCTAGTCCCCTTCTCATCAATCAGGACCAAGCCAAAGTGAAGAATCTTGTCATCATCCTTTTGGTCACAGAAAGCCCAAAATCGCGAAACCCGAACACAAATGCGCTCGTTGTCGTCACCAAGGGAGAGATCAGAGAGCAGGGTGTGTCCCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.984348
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0009400.4 osa-miR5534a Cleavage 3.5 19.745 1 21
Osa01LNT0009400.4 osa-miR5534b Cleavage 4.0 19.745 1 21
Osa01LNT0009400.4 osa-miR812r Cleavage 4.5 19.117 1 24
Osa01LNT0009400.4 osa-miR168b Cleavage 3.5 16.944 1 21
Osa01LNT0009400.4 osa-miR169f.2 Translation 4.0 18.844 1 21
Osa01LNT0009400.4 osa-miR169p Cleavage 4.0 19.379 1 22
Osa01LNT0009400.4 osa-miR1855 Translation 4.0 17.908 1 21
Osa01LNT0009400.4 osa-miR1428e-3p Cleavage 5.0 12.239 1 21
Osa01LNT0009400.4 osa-miR1860-5p Translation 4.5 23.541 1 21
Osa01LNT0009400.4 osa-miR2104 Cleavage 4.5 14.192 1 22
Osa01LNT0009400.4 osa-miR5150-3p Cleavage 5.0 23.162 1 24
Osa01LNT0009400.4 osa-miR5501 Cleavage 4.0 14.909 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0009400.4 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0009400.4 1 gp1 Morphological trait Panicle/flower RG532 RM259
Osa01LNT0009400.4 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0009400.4 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0009400.4 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0009400.4 1 nan Resistance or Tolerance Other soil stress tolerance C955 C885
Osa01LNT0009400.4 1 An9 Morphological trait Panicle/flower nan nan
Osa01LNT0009400.4 1 nan Resistance or Tolerance Lodging resistance R1944 C955
Osa01LNT0009400.4 1 nan Morphological trait Root RM7383 RM243
Osa01LNT0009400.4 1 nan Morphological trait Root RM7383 RM23
Osa01LNT0009400.4 1 Rf Physiological trait Sterility nan nan
Osa01LNT0009400.4 1 ppp1.1 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0009400.4 1 prg1.2 Physiological trait Source activity RG140 RM243
Osa01LNT0009400.4 1 spp1.2 Morphological trait Panicle/flower RG140 RM243
Osa01LNT0009400.4 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0009400.4 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0009400.4 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
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