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

>Osa02LNT0167800.1

CTACGTGGCCCTATTTACATTTCAAAAGTAAACTAAGCGCACAAAAGTCCTAGGGCGTTATTATAGCAAGGAATTTACCATGTTAGGCTGGCTTCTGGCTGGCTGGTGGATTCACCTTGCTAGCCCCGTTCACCGCTGTGTTGGCCCGGTTGTTGGCTGGTGTTACGGTGCCAGGCGCCACATTCTTGGGCACTAACAAGTTGCCCTTTGAGCTCATGCTTTGCTGCTTCTGGACAGTACTTTGGGTGCCTGTGGTAGCAGGAGCAGGTGCCTTCCCTCCTAATGATCTATTCAGCACGCCAACTATGCCGCTAGACATCCCACCCTGTGGAACTGGAGCTTTGGTCTTTTTCGCAGTTGCTGGAGGTCCAGCAAATACAGGGTTGCTTTTGCCAACTGTGGGCAGCGTCTTCAGCTGTTTTTTCTGGCTGCCAATAACGCTTTGAGCTTCTGGAGCAATCTTGGCAGCCTTGCTCTTATCCACATTATCCTTATTTAAGCATCCTTGGGCCACAAAGCGATCAAATTCTAACATGTCTGCATCCTTGGGGTCTATGGCCTCCTCAATCTTGGGATCTTGAACATCTTCCTGCTTCACATCCTCAGGGAACAAGTCCTCCATTGTGACTGCAAAATAATTAGAGTTGTCATCTATTTCCATTTTGTCAGAAGATCCAGACACTGGTGTGGTGTTCAGTGCTTTCTTAGTTTCTGATAAATGCACTCCAGCGGATTGTCCCAGAGGATTAACCCCAGCGACTTCTGAAACATTATGAACTTGTTCAGTTGCATGTGCAGTCAAAACTTGAGATGGACCACCAGTACTTTGTAATTCTAGGTGTTGATCACTGCCAAGCTGTGTCCCAGGTTCACCAGCCACAGTAGGTGTTTTAGATCCCGTAGAAGATTTTGAAGATCCTGTTCCTCGAGATCTTATGTGCACAGCTTTTGTGGACTGTGCAGCTTTTAAAAAATTGGTGGCAACACTTGGTTCGGCAATTCGCCCACCAGCAGCAAGAGCTGCCTCTTGTATCGACAAAGGGCCATTCACAGGAATTGATTGGGCAACTTGTTTCTTAGAATTATTTCGTGACTTATTTGAAGCATTTGATACTTTTGGAGGTGGAGGTGCAGATTGCGCAGGTGCTTGATGCAACTGAGGTGGTGGTAACTGCACTTGTACTGGTTGCACTGGAACAGGCACCGGAACAACATGCACCGGTACCGGCAATGGTGAAGGTGCTGTAACAGATTTCACCTCAGGATTCGTAGTAGTAACCATTGGATTGTGATGTGGCACACCTCCTGGTCTTAATGTAGACGATCTGGTCGTCCCAATGGCCAATGAAAATGCTTTTTGTGCTGCCTTTAGTTCCTCCGACATAACATTGGGTATTTTAGGGGTAGCAGGCTTGGTTGACCCCTGACGCTTGCAAATAAGCGCCCATCTCTGTTGAAGTTGAAGATGCGTCCTTGAACTATCAAATTTATATTTATGCAGAATTTCCATCCAATTTCCTTCACCATGCTTCTGTACACCTGCTCCTAGTTCCATGTCCTCCTCTCTGGACCATGGTTTAGGCTTCTTTTTCTTTTTGGGATGTCCATTAGGGTCCAAAGGATCAGGAGATGAGCCTGTGTGGGAGGGCTGCTTTGAGCTGGAAACCGGACCTGTACCGTTTGTTAGACGGTGACCAGGCACAAGCTGTTTATCAGATGGAACACGCACTATCTTTTCATTTGGAGTGTTTAGCGCAGCAGCTTCTGAGTTGACACGTTGACCAGAGGTTTGTTCACGTGAAGATCCGGTGATAATAGTCTTGGCAAACGATGTGGCCTCAGCTAATGCTTCATTACCCGGAGCAGGGACAATCTCAATCTCACATTCTAGATCACTCCCATCGTCCTACGAATTATCGGTCACAGCAGCACAGCACCATCAGAGAAACGAACAACCAACACTGAAAACAAGCTGAGATCTACTTCTACTACTGTATAAAATCTCAACAATTTCCCGAATATATATAAAAAAGTAACAGAAATCTCGGCGAGTGGCGAACCAGCGGCAGGGAGGCGGGCTCGACGCTCTCGACGAACTCGTGGCCGTAGGCGAGGTGGCGCCACAGCATCTGGTACTCGCGCGCGGAGGTGATCCCGGTGCTCGTCCTCCGCACCAGCGCCCTCCAGTCGATCCCCTTCCCCGCGCCCACCTGCTTCCCCATCTCCTGCAGCATCGTCAGGATCGTCGCCGGCTGGTACCTGTGCAGGATGAGGTAGGCGTCGTCCTCGGAGAAGCTGCGCTTCCGCTTTGCCGCCCCGCCCCCGCCGGCCGCCGCCGCGTCCATCTCGGAGTGTAACCGACTCGTCGGCGCTTGGCCGGGGAACTCCTTTTTCATCTCCTTTTCTGTTATTATATTATTTTTTCTCCCCTTCTTTTTTTTTTCTCGATTTGCTTGTTGATGAGAGCGAAGAGGGGATGAAGAATTGAAGATAGTCACATAGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.849392
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0167800.1 2 20764778 C T
Osa02LNT0167800.1 2 20764785 A G
Osa02LNT0167800.1 2 20765221 G A
Osa02LNT0167800.1 2 20766038 C G
Osa02LNT0167800.1 2 20766116 A C
Osa02LNT0167800.1 2 20766982 G A
Osa02LNT0167800.1 2 20767401 G C
Osa02LNT0167800.1 2 20765225 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
Osa02LNT0167800.1 osa-miR166k-5p Translation 5.0 23.888 1 21
Osa02LNT0167800.1 osa-miR166l-5p Translation 5.0 9.347 1 21
Osa02LNT0167800.1 osa-miR172a Cleavage 5.0 17.975 1 21
Osa02LNT0167800.1 osa-miR172b Cleavage 5.0 17.975 1 21
Osa02LNT0167800.1 osa-miR172c Cleavage 5.0 17.975 1 21
Osa02LNT0167800.1 osa-miR172d-3p Cleavage 5.0 17.975 1 21
Osa02LNT0167800.1 osa-miR2092-5p Translation 5.0 16.566 1 21
Osa02LNT0167800.1 osa-miR2919 Cleavage 3.5 17.252 1 19
Osa02LNT0167800.1 osa-miR5083 Cleavage 4.5 21.27 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0167800.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0167800.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0167800.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0167800.1 2 qRTH-2 Morphological trait Root RM262 RM341
Osa02LNT0167800.1 2 qSTA-2 Morphological trait Root RM262 RM341
Osa02LNT0167800.1 2 nan Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0167800.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0167800.1 2 qRTT2-1 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