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

>Osa04LNT0266500.1

AACAAGTATTGACGTCTGGTTGGTTGCCCCGTACGCGCAGCCAAGCCACAGCCTCACAAACACGACACCAGCAAGGTCATCGCGGCAGCGGCTCCGTAGCTCGCGGCCTTGTGAGCCACCACCGCCGGTCCGGACGCCGACCTCTTGGCGCCGCCCTTCCCCGCCGCCGGGTCCGGCGGCGGCGCCGGGACGTAGTCGTCGATGTCGCCGTCGTCGTCGTCGGGCGGCGGGTGATCGGCGTGGGGCGGCGGCGACGGCAGCGCCGGCACGGGCGGGGTGGCCGCGACGGGCGGGTGGGCGTGGAACAGCGCGTCCGGGAGCAGCACCGTGTCCAGCTCGTACACCGCCATGGCCGCCGACTCGTACACGCTCCCGACCACCCTGGCGCTGGACCACCTCGACATCACGTGGACCACGCCGCCGTCGTACGTCACGTTCACCGCGTACCTCCCGCCGGCGAGCGTCTTCACCGGGTTGCTCTGGCTCAGCCCGTCGAACTCCGCCAGCGTGTAGTGCTTCGCCAGCGAGTGGTACATCAGCAGGTGCTTCAGCTGGTTCCTCGATAGCCCCGCCAACACCGATGGCTCGATGGCGGCGAAGGCCATGTCGACGGGGACGAAGATGGTGATGCCCTGGTGGGTCCGGTAGGCCTGGTGCTCGAACACCGCCACGAGGTTGGTCTGCCGGAGGTACATGAGGAAGGTGCTGAAGGGGCCGGCGACGTTGAGCACGTCGGTGAGGTTGCCGCCCTTGTCCTGCGGAGCCGGCGCCGCGCCGCCGCCGGCATCCGTCCTCACCGGCGCCGGGGGCGGCCGGGCAAGCGCGCCGGCGAGCAGGAGGGAGAGGGACAATGCGATGGCGAGGAACGTCGCGACGGCGAGCCTCATTGTGACAGATCGACTGATAGTGCAGCTGCCGCGCTATCAGCTGTGAACTTGGCTTCAAG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.677719
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0266500.1 4 23598916 T C
Osa04LNT0266500.1 4 23598930 G A
Osa04LNT0266500.1 4 23598954 A G
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0266500.1 osa-miR5805 Cleavage 5.0 19.043 1 24
Osa04LNT0266500.1 osa-miR7695-3p Cleavage 4.0 22.907 1 21
Osa04LNT0266500.1 osa-miR2102-3p Translation 5.0 21.565 1 22
Osa04LNT0266500.1 osa-miR3980a-5p Translation 5.0 23.637 1 21
Osa04LNT0266500.1 osa-miR3980b-5p Translation 5.0 23.637 1 21
Osa04LNT0266500.1 osa-miR5154 Cleavage 5.0 24.349 1 24
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0266500.1 4 orl1 Morphological trait Culm/leaf S10628 C377
Osa04LNT0266500.1 4 qChla4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0266500.1 4 qChlab4-1 Morphological trait Shoot/Seedling C2807 RM241
Osa04LNT0266500.1 4 qPH1-4-1 Morphological trait Dwarf RM241 C2807
Osa04LNT0266500.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0266500.1 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0266500.1 4 qDLR4 Resistance or Tolerance Other soil stress tolerance RM3524 RM3866
Osa04LNT0266500.1 4 d11 Morphological trait Dwarf nan nan
Osa04LNT0266500.1 4 nan Resistance or Tolerance Other soil stress tolerance RM5586 RM3916
Osa04LNT0266500.1 4 nan Morphological trait Culm/leaf RM3337 RM3785
Osa04LNT0266500.1 4 gpp4 Morphological trait Seed RZ569 RZ565
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