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

>Osa02LNT0167900.1

CTCCTACAATATACAATGGCGATTAATTAATTAATTGATCATGTATCAATCACACCCTAATTAAGCATCCATCACCGATCTTGGTTTCTCATCATCTGGCCATCTCCATTTCTTTCTTGATTTTTTTTCTCTTATTTTTTCTCACGGTTTTCCGGCGTCGCTGCGTTTGAGCAGTGGACAGTTTGAGCAAAATTTGCGGCGGAGAAGAAGATGGTGGCTGTGACGTCACGGTCACTGCCGCTTCTGTGCATCCGCCAGCGCCTTGATGCCGTCGATGTCGAAGTCGACGGCGGGCGACACCACGGCGGAGGAGGGCCTCCTGCTCAGCGGGAAGAGCTTCCCGCCGCCGCCGCCGCCGCCGCTCCGCGCCGGAGCATCGTTGCTGCTCTTGCTCAGCCTGTCGTTCTTGCTCAGCTGCGCCGCGGCTGCCACCGCCGACGAGCTGTCGCCGCCGGCGCCGCCGCCGCCGCGAGCTGACGACAGCTCCTGGCTCCTGCTGTGACAGGGAGCGCGACGCCGGCGGCCCGCGTACACGTCCTGGAGCATCGCGCGGTCCTCCCTGGTGAGGCCACCGCCGGTGCCGCCGCTCGGCCTCGCCACCGCCGGCGGTGGCGGCGAGGACGACGACGTCGTCGTCGGCACCTGGTGCGGCGGCGTGAGGGGAGGGGAGCGCACCGGCGACCTGCTCGGCGACCTGGACCTGCCACCGTTGCTTGGGCGGCTGTAGCTGATGAGGTGGTGAAGCCACAGGACGAGGTCCAGGATGCACGCCTCCGTCTTGGCCTTGTCCGCATGGTAGAATGTCTCGATCTTGATCACGTCTGGCTGCCCAGCCGCCCTCCGCATCGCATCGTTCCCTGTGTTCGCCCACTCGCCGACCCATCCGAATCCATGGTGAGCTCTGGCTGTATTGTTGGCAATAGGGATAATCCATTGCAAGGTTCTCTCCATTGAAGATCTGATTTCAGTGATCGGAACCTCTTGTGGTTGTGGGCAATTATGTAGTTTTTTTCGAAGAGCAGACTTAATAGTTGGGGGCAGTCCTTGATAGAGCGCATCTCTTGTGCTTTGTGGTGGAACGGTGCTTCGGGAAACAATGTTGTCAATCTGTGAAATGATATTGGCATAGTGCAGCGAGAGGCCAGCTGATCCTAACGTCTGACGGCTCTCTGAAGGTTGATTCAATTGTAAAGCTCCATCATAGGTCCCAAAAGATTCTTGAATCTCTACATGTAAAAAGTGGACAATATCCACAAGTTTATCCATGACGTCTTCGAGCATCTTATTCCAAAGGGACTTTTTCTTCAAGCTTTTCACATGCCTCCTTTGGCTCTTCAATTCTTGCCTTATAATCTGAACAGTGTCCCCTCTTTCAAAAGCAACTGATTTTTTCTCTTCCTCCAATTTACGGCGATAATCTTGCTCAAATCTATCTAATGCATGCAACTCATGGTACAGATCAGCCGTGTGCCGAACCAGTGTCAACAATTGCTGCATCTCTGCTTCTGCTATTTCTTTCAAGTTTGGTTGAGGCGTAATTTCTGATTCTAGCTTGGAAAAATAGCGATCGAGGTTGTGCCACTGAGTATCCTTGCAACGATTGCCAAATCTGATCACCTCTCGCGAAAATAGCGCCAGCTCTTGCCTCTTGTCGGCTGCAGCAATTCTCATCAACTCACTCATATCGCTAGAAACCAAACGCTTTACGCCCTCCGATCGGAGGACGGTCCCCTTCAAGTATCTGACGCTTTCTTTGGACAGAGACTGCATCAGGCTCATGCCCTTCACTATTGTGTTGGCAACCTCAAACGCAAGAATCTTTTGTGGGCTCCCCTTCATCTTCGCGCCCGCCACAAACCCACCTACAGGGCTCAAATTCGTCATGCTGCTGCTCAGTGTGTCCAAAACCTCCACTGCTTTCCCAATCCCAGATGTGCTGGCTCTACCAAACACCGAGCCTTTGTCTGAAGCCTTGCCGGAGGTGCTTGTCCTGGACTTGCCGGCCTTGAGCTTCTCCGACGAGGAGCGCACCAGCTGCGGCTCCTTGGAGACCGACCGGCGAGCCTTGCCGCCGCCGCCGCCGGTGGACAGCCGGGGGGCCTTCTCGGGGGAGAGGCGGCGCGGCGGATCAGGCTCCGGCGCCACCTCCACCGGTGCCGTCTTGTGCTTCCCCTGCACCTTGCCGGCGACGGCCGGGAACGCCTTGAGCTCCTGCTCCACCACGAGCCCCATCGCCCGGAACGACAGCTCCGCCGGCGACCTGTCCCCCGGGATCCCCGCCGAGCACACGCCGCCCATCTCGGCCCCCAACACCCAATGCGCCGCCGCCGCCGCCGACGAGCTCACAACCCAAACACCTCCACCACCGGAATCCACCGCCGGCGATCGACAACCAAACGAGCAAAACAGGATCCGCGCCAATCCCACCACCGCAATCCACTGCCACTGGACGCCGCAAAGATCGCGAACACCACCAAGAACGCTAAGTCTCCCGCGTTGCCGACGACGACGACCACTACCACCACCACCACCAAGAACGCAAAAATCCAACTAAACCAAGCGAAAAGAAATAGAGGAGAGACGAGGCGAGGCACCAAACAAGGGAAGAAGAGGAAGGAAGGCGCGGATCGCGTGCGAAGTCGTCGCCGCCGCCCGCCGCCCGCCCGGTTTTAGTCAACAAAGCCGGGCGTCCGAGACCAGATTTTTCTCGCCCCGCGGCTGCGCCACCGCCAACCCCCCCGACAGCGAGAGAGCGCGCGCCGCCGGTGTGGCCGGACGGCGAGGTTTCTCCGGTGTGATTTGATCGGAGTCGGAGGAGGAGGAGGAGGAGGAGTGCTCGCGATCGTCGCTAGGCGAGGCGAGCTTTGGGTGGGCGACTTTTTGTGGGTTTTTTG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.204062
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0167900.1 2 20783470 T C
Osa02LNT0167900.1 2 20782741 G T
Osa02LNT0167900.1 2 20782760 C T
Osa02LNT0167900.1 2 20782804 C G
Osa02LNT0167900.1 2 20784362 A C
Osa02LNT0167900.1 2 20784379 A G
Osa02LNT0167900.1 2 20784823 T C
Osa02LNT0167900.1 2 20784493 C A
Osa02LNT0167900.1 2 20786894 A G
Osa02LNT0167900.1 2 20787196 A G
Osa02LNT0167900.1 2 20784422 G C
Osa02LNT0167900.1 2 20783627 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
Osa02LNT0167900.1 osa-miR5527 Cleavage 4.5 20.217 1 21
Osa02LNT0167900.1 osa-miR5817 Cleavage 2.5 21.268 1 24
Osa02LNT0167900.1 osa-miR5834 Translation 4.5 21.989 1 21
Osa02LNT0167900.1 osa-miR7694-5p Translation 4.5 21.186 1 24
Osa02LNT0167900.1 osa-miR395t Cleavage 4.5 15.918 1 21
Osa02LNT0167900.1 osa-miR395c Cleavage 4.5 15.918 1 21
Osa02LNT0167900.1 osa-miR395a Cleavage 4.5 15.918 1 21
Osa02LNT0167900.1 osa-miR395u Cleavage 4.0 15.918 1 21
Osa02LNT0167900.1 osa-miR2867-3p Translation 5.0 11.171 1 20
Osa02LNT0167900.1 osa-miR2926 Translation 4.5 16.491 1 20
Osa02LNT0167900.1 osa-miR3982-3p Translation 4.5 22.137 1 21
Osa02LNT0167900.1 osa-miR5340 Cleavage 4.5 15.713 1 23
Osa02LNT0167900.1 osa-miR5499 Translation 4.5 14.255 1 21
Osa02LNT0167900.1 osa-miR2275c Cleavage 3.5 9.533 1 23
Osa02LNT0167900.1 osa-miR2275c Cleavage 5.0 7.712 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0167900.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0167900.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0167900.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0167900.1 2 qRTH-2 Morphological trait Root RM262 RM341
Osa02LNT0167900.1 2 qSTA-2 Morphological trait Root RM262 RM341
Osa02LNT0167900.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0167900.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0167900.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
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