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

>Osa04LNT0265100.1

CACCGAACACCCTTCAGGATAATTCGTATACAAAACTTGCAGGTACACAACTAATTATGGTCCAATTCCTAAGCTGCGTAAACGGTGGAAATGTACATACAAATTGTCAATCGAACAGTCCTCATGCCATCGAAATGCTTCTGAATTTAGTTAAAATAAAATGCTTCTGAAGAGAACCATCCCATCACAGCTCGCATACAGAACACCCTGCTTGAATTCAGAGGATAAAAACATCATTATAACAAGAAAACTAACAAAGAATCACAAGGGGCACGTACCTGTTAAATCTGTGTTAAATCCTCTTAAAAGGATCAGTACTGCATCTTTAAGTTCACATTGAACCTTTTGCTTCGGTAACAGCTGACAGATCTGACTTGTGCACTCTGCAGATACTTTGTAGTTAATCTAGCTTGGTGGGACTTGGGAGCATTTTGTTTAGACAAACAAGTTTTTTATCTGACTTGTGCACTCTGCAGATACTTTGTAGTTAATCTAGCTTGGTGGGACTTGGAAGCATTTTGCTTAGACAAACAAGTTTTTTACCTGACTTGTGCACTCTGCAGATACTTTGTAGTTAATCTAGCTTTGGTGGGACTTGGAAGCATTTTGCTTAGACAAACAAGCTTTTTACAATAGGGGGTAACACCCCGCAAAACGAGGACTGATAATGGAGTACCAAATTCAATAGAGTTGGTAGCTCATCGTCTTATCTGGAAAAAAAACTGTCTTCAAACTGGAAAGATAATACTACTTCCCTTATTTGTTTACAACAAATTTCTTTGTTTGCCTCTTGTTACTTCTTTTACCATACACAATAACTTCCTCAGTTCAAATAGTCTTCTTGTCTAATGTAATTGAGTTTCCTTTTTTTTAAAAAAAAACTAGTGAGTTGATAACCCAGCATGTTTCTATGGGTATACACAACATATTTATATTGCTGCTTTTGGCAAACCTGGATTCTGCATTTCTTGACTCTGTTTTCATATCCAATAGTTCTGGCAAAGGGAGGCAGCAAGCTTGAGACAACAACTGCACAGCTTGCAAGAAAATCATCGGTATGGCCATAAAACCGATTTTCTTGCAAGATATGCAGTTGCTGTCTCTAGCTTGCCGCCTCCACTTGCAGCAACTGAGAAGCCGGCTCGAAGGTTGAACCCTAGATGAAGAGAGGCGGGTCGCTAGGCGGCACAGAATCAAAATCAACGCAAGCATATCGGCTGGGGCTACAGCCTACAGGAGCGGCAATGGGAGAAGCTAATCGGGGAGCCAACGGCCACCACGATCCGAGGGTCGTGGTCATGCGACGGGCGGC

Coding Potentia
Explanation CPC Score
noncoding -1.27461
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0265100.1 4 23045762 A T
Osa04LNT0265100.1 4 23047492 G A
Osa04LNT0265100.1 4 23047812 A T
Osa04LNT0265100.1 4 23049315 T A
Osa04LNT0265100.1 4 23049844 T A
Osa04LNT0265100.1 4 23050652 A G
Osa04LNT0265100.1 4 23051082 G A
Osa04LNT0265100.1 4 23051133 A G
Osa04LNT0265100.1 4 23056001 A G
Osa04LNT0265100.1 4 23056196 G A
Osa04LNT0265100.1 4 23055016 A G
Osa04LNT0265100.1 4 23046635 A T
Osa04LNT0265100.1 4 23051883 A G
Osa04LNT0265100.1 4 23052106 A G
Osa04LNT0265100.1 4 23054423 G A
Osa04LNT0265100.1 4 23050883 A G
Osa04LNT0265100.1 4 23051597 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
Osa04LNT0265100.1 osa-miR535-3p Cleavage 4.5 19.659 1 21
Osa04LNT0265100.1 osa-miR2874 Translation 5.0 12.044 1 24
Osa04LNT0265100.1 osa-miR5505 Cleavage 4.5 15.175 1 22
Osa04LNT0265100.1 osa-miR2098-3p Cleavage 5.0 11.536 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0265100.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0265100.1 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265100.1 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0265100.1 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0265100.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0265100.1 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0265100.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0265100.1 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0265100.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa04LNT0265100.1 osa-MIR444b 86.765 136 2 137 2.81e-35 145
Osa04LNT0265100.1 osa-MIR444c 100.0 138 1 138 1.24e-68 255
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus