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

>Osa07LNT0390500.2

AAAAGGAATCAATTTCCAGATTGACAAATTAATTACAGATGTATTCACCATTAGCTGATAGGTAATTGCCTATTACATATACACTACAATTTGGTTTAAATCAAAACCACGATGAAGTTACATCACACACCAGCATATATAGTCTCTTCCCAGGTGTATCAAAGAAAAAAGAGAGAGGAACAAATTGAACATCTCTTGTCTGAAGAAAGGAAACATGCATGCTTCCCCTTGTTCTGTCGGTTGACTTGAGTGTCCTAGCTTGAGTGTAACTTCAGATCAGAAGTAAAACTTTTTAATCATATATATTCATATGACAGTATTATACTATTATCTATGCAAAACCATTAGTGATAGTTTGCGAGCTGTACTTCATATGCAATGGAAGGTCAAATACGGTCAAATACGAACCATCAGCCATCTGTATAAACTGCTTCTTCCCAGACTTTGGTGTTCTTTTTAGGGTCATCGCAAAGAGAAAGGTCATTATCGAATTCTTTCATGGTCTTCACAAACTTCCTTGCTCCTTGCATGATTAACCTTTCGACCATGAACAGCTGATAGTTGTTATCGATTACTGGCTCCAATATGCTGCTGAAGTTTGATGAGTATGCTAACTTGTATCTGTCTGATAGAGGTGAAAAGAAGCCTGGTGTCCTTTCATTTGAAGCAATGAAAAGAGTACGGCCTCGCGGAATCCACTTTGCAATTCTTCTTTTGATGTTCTCAGGATGGGTATCTCTGTCCAGATGAGGATGAAGGCTTCGCTCAACACCAAATCGATCTTTCCTATTCTTCAGTAGATCACCCCGTCTTACATGAATAGCATCGTAGTCACCAAGTATCACTTTAATCTTGTTTGCTGCATCCCTCAGTTTTCTTGCTGGCATAGATGGCAGAAAATTGTATGGTAACATCACAGAGCTACGCTTGGTCCGATCCTTGCACTCCATAAACCTGAACAAGCAAGAGGACTTGCGGTGCGGTTTATGAGGAATGCCTTTGAGTAAAGTGTGTTTTCTTTGAGTTCTTGTCTGCTAACTCCTTGTGCATGTGCTACATCTCCTTCCTCTCCTAGCTTCGTACTTCTTGATACTATAGCATACCATGATTGTGGATTGTCCAAAACAACAGGAACAGTTCTTGATATGAGGTCTATGTCATACAAAGATTCCATCGCACATGAACTTGTTTCCCACCTGCCACTTTTATTGGAAGTCGCATCGCTTTGATTAATAATCCCCCTTGTATTGTGCACTGAATTAAGGCACAACCTTGAAGGCATCACAAATATTCTGTCAAGAAACAGGGCCTCCTCGAGGGCGCAGCGGAGGCTGGACTCCTGGTGGCCGAGGCCGGCGCAGGAGGCGCAGTGCTTGCCGGGGCAGTCGATGGCGGCGCCCCAGTAGAGGTAGCTGCGGCTGCTCTCCCTCTTGTCGACGCCCCTGACCTGGAACCCGAGGTAGGACAGCGAGTCGGTGAAGGACAGCACGCACAGGATGGACAGCACCGACGCCGTCGTCACGGCGGCCAGCAGGGCGCCCTTCGGCGGCAGCGGCAGCGCCATCCGCTGCCTGCCGCCGCCGCCGCCGGCGGTGATCCGGTAGGGGATCGCCATGGGAGAGGAGGAGGCGAAGGTGGTGGGGGAAATG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.699164
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa07LNT0390500.2 7 26678056 A G
Osa07LNT0390500.2 7 26677777 G A
Osa07LNT0390500.2 7 26678572 T C
Osa07LNT0390500.2 7 26678956 T C
Osa07LNT0390500.2 7 26679504 T C
Osa07LNT0390500.2 7 26680214 C T
Osa07LNT0390500.2 7 26680289 G A
Osa07LNT0390500.2 7 26680312 G 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
Osa07LNT0390500.2 osa-miR156l-5p Translation 5.0 13.837 1 21
Osa07LNT0390500.2 osa-miR156l-5p Cleavage 5.0 19.936 1 21
Osa07LNT0390500.2 osa-miR1861c Translation 3.5 17.408 1 22
Osa07LNT0390500.2 osa-miR1861e Translation 4.5 17.408 1 22
Osa07LNT0390500.2 osa-miR1861k Translation 4.5 17.408 1 22
Osa07LNT0390500.2 osa-miR1861m Translation 4.5 17.408 1 22
Osa07LNT0390500.2 osa-miR1861n Translation 5.0 17.408 1 22
Osa07LNT0390500.2 osa-miR2863b Cleavage 4.5 15.286 1 21
Osa07LNT0390500.2 osa-miR2928 Translation 4.0 16.03 1 20
Osa07LNT0390500.2 osa-miR2929 Translation 5.0 12.037 1 21
Osa07LNT0390500.2 osa-miR2929 Cleavage 5.0 22.353 1 21
Osa07LNT0390500.2 osa-miR5076 Translation 5.0 20.648 1 22
Osa07LNT0390500.2 osa-miR5505 Cleavage 4.0 18.161 1 22
Osa07LNT0390500.2 osa-miR2275c Cleavage 4.0 13.054 1 23
Osa07LNT0390500.2 osa-miR810a Translation 4.5 21.628 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa07LNT0390500.2 7 hd7a Physiological trait Flowering RM18 R1789
Osa07LNT0390500.2 7 qLVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
Osa07LNT0390500.2 7 nan Physiological trait Eating quality R1245 R1789
Osa07LNT0390500.2 7 qPLLN7 Physiological trait Sterility RM234 RM172
Osa07LNT0390500.2 7 nan Resistance or Tolerance Other soil stress tolerance R1245 R1789
Osa07LNT0390500.2 7 qCIVG7-2 Resistance or Tolerance Cold tolerance RM336 RM118
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