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

>Osa04LNT0267100.2

CACGCAAAACATATACTCTTTTATTATTCAATGAGAAAAGCAATGAGTGCAATGGTGCTTTTTTATCATTTCAGGAGGAACTTCTTGAACCAATGGGCAGAGTTCTTGGGGTATCTCTTCCTTCCGTCATTGTAATCTACGAAGTTTATCCCAAATCGAACTGTGTAGCCGTTCGACCACTCGAAGTTATCAAGCAGCGACCATGCAAAGTATCCCTTCACGTTTGCTCCATCCCTTATAGCACTTAGCAGGGAAAGGAGGTGCTTGTGGTAGTATTCTATCCTAGCGTCATCCTTCAAGGCTTCTTGGAGTGGTAAGGTCTTATTGTTGAATTCATCAACGCCATTTTCAGTGATGTAGACGGTAGGATTGCCATAGTTCTCCTTAACATAAAGTAGCAAGTCACGGAAGCCTTGAGGGTAGACGTAAAGCCAAGGTGAAGCAGCCTGCGGTCCTATGGGGATGCCATTTCGTACACCGGTAAGATTAGCTCGAGAATCGGTGGTATAGCTGTTGTTAAGGCCATTTGATGGAGGAAGGTTATCAGCATAGTTCGCAGTGTAGTAGTTAAGTCCAATAAAGTCAAATGCACCCTTGACCAACTTAGACTGTTCTTTAGTGAACTGTGGCAAGCGATTCCCAACCAATCCTCTCATGCTTAGGGGGTAGTCGCCTCTAATGAGGGGATCCATAAACCATCCAAACATGAAGTCTATAGCACGCTTTGCAGCATCATCGTTGGATTTGGAGCGGGAGAAGGGAACAAACCAGTGCGAGACCAGAGTTATTCCAATCTTCCCTTTTTGTAAGGCCTGATATTTCGCTTTGTACAACCGAACAGTTTCCGCGTGGGCAAGTAGTTGATGATGGCATGCAGTGTAAGGCTCCCTTCCTGAATCTCCAACACTGCAATTTCCCTTCTCCCAGGGCGAACAACGGCCTGGTGCAAACAGGCCAGTTGCATAGCCATTAGAGCAGAAAGTCCAAGGCTCATTGAAGGTGATCCAATTTTTCACTCTGTCACCAAACTCCTTGAAGCAGATTTCAGCATAGTCCTTAAAGTCATTTATGATATTAGGGCTAAGAAATCCATTATATTTATCTTCCAACGCCTGAGGTGAGTCCCAGTGGAAAAGGGTAATAAACGGTTGCACCCCTTTCGATAATAGCTCATTGATCAAATTATTGTAGTACTTTATGCCTTCTTTGTTGACTCCACCCCTCAGACTTCCATTTGGAAGGATTCTTGTCCATGAGATGGAGAACCTGTATGCATCCATTCCCATATCCTTCATGAGGCGCACATCTTCCTTGTAGAGATGGTAGGAATCCGAAGCCACATCCCCGTTGCTTCTGTCGGCGATTTTCTCTGGGTGCTGATGTGTGAAGGTGTCCCAGATGCTTGGTCCTCTGCCGCCCTCCGCTGCGCCACCCTCGTACTGATACGACGACGAGGCTGTCCCGAAGATGAACCCCTTGGGGAAGCTTCTCCGGCTGACCGGCGGCTCGCCGGCGCCATTGTAGGCGCCGGAAGCGACGACAGCAAGGAGGAGGAACGTGAGGAGAAGGCCACCGGGCATTGCCCCTGCTGCCGCCATGGACAGAAAAAGGAAAAATAGAGAGATGGCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.983891
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0267100.2 4 23750382 T C
Osa04LNT0267100.2 4 23749522 A C
Osa04LNT0267100.2 4 23749919 C T
Osa04LNT0267100.2 4 23750013 T A
Osa04LNT0267100.2 4 23750766 T G
Osa04LNT0267100.2 4 23752029 A G
Osa04LNT0267100.2 4 23752113 C G
Osa04LNT0267100.2 4 23749240 G A
Osa04LNT0267100.2 4 23752450 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0267100.2 osa-miR5512b Cleavage 5.0 23.254 1 21
Osa04LNT0267100.2 osa-miR397a Translation 4.5 17.609 1 21
Osa04LNT0267100.2 osa-miR397b Translation 5.0 17.609 1 21
Osa04LNT0267100.2 osa-miR416 Translation 5.0 12.955 1 21
Osa04LNT0267100.2 osa-miR1854-5p Cleavage 4.0 11.994 1 21
Osa04LNT0267100.2 osa-miR812k Translation 4.5 19.852 1 24
Osa04LNT0267100.2 osa-miR812l Translation 4.5 19.852 1 24
Osa04LNT0267100.2 osa-miR812m Translation 4.5 19.852 1 24
Osa04LNT0267100.2 osa-miR5083 Translation 4.5 9.224 1 20
Osa04LNT0267100.2 osa-miR5512a Cleavage 5.0 23.254 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0267100.2 4 gpp4 Morphological trait Seed RZ569 RZ565
Osa04LNT0267100.2 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0267100.2 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0267100.2 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0267100.2 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0267100.2 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0267100.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0267100.2 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0267100.2 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0267100.2 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0267100.2 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
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus