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

>Osa02LNT0170500.1

CCTCAAAGGCTCAAACCAGCAAAGATCAACACAAACTAATTTTTTTTTACAGATAGCAATGCAATCCAATGATCCATCACCCCCTAGGCTACACGCTATTTATACACCTCTTCACTCCTCTTCTCGCTCACGGTACAGAGTTACAAGCCACTGACAAAACCGACAAGCCATCTTACCTGCTACAGGACCAACAAAAAAGAAGAAGCAGGGTATACATATATGGCGTGCAAATCAGACACTTCGGTGGAGTTACAGATAGATTTCGACCGACTTCAGCAGCGCATCAGAATTTCAGAGATTCTTCAGGAGGTATAAGAAAAGGGGATGCTCAGAATTTCCAGCAGAGGAAGCCCTTATTCCAGCCACGGCGCCGCTTGTTTCGCCTCCGCTCCGCTCTCGCCATCCTCACCGGGCTGCTGTTCCAATCCCACTGTAACACTGGAAATGCGAAGGACCGGGTGCTTGTCGTGCTACTATCTGACCGGATGGAGATGTTGCCAATGTGACCAGAGGTCGACACTGGGTTGCACATGATGCTAGGCCCAAGAGAGCATGGCTCAAGGGGATACCCATTGCCAATCAGAGATTTTCCCTTTGCATTATTATCAGGCACATCTAGTTCATCCACATGAGTGGAATCCTTTTGCGCATCGGTAGAACTCGTGCTAATTCTGCCATCGTTTGTTGCGTCTGCGCAGCTCTCTGAATCTGTCTGGTTGAAATCATGCACATCAGTAGCACCATCGTTGTCAGAGTTCTTGTTGTTCATCTGCCTATTTGCATCACTGGACTCTACAACATGAGGTGATGAGGATGTGGCCACTGCATTTTCATCCTGTGGATCCGCTATCGGCTCGCTGGTGAAGCTTTCGGGGTGGTCGTTGCTCTTTTCGGATGGTTGGACTTCTGAAGAACTACTTGATGTCAGAGCATCAGGCATGGCTTCTGCTGTTCCAACTTCGTTAAATTGTTTGGAGCCAATTAAACCGTCAGTAGTCTCAGCAGTGGACATGGGTTTATCTAATGCTGCGGTTGCATCATGTCTGTCAGATATTGTTGCTGATGAACCGTTGGTGTTATTGATACTTGATACGTTGCTAGTAATAAGTTCATCAGTTTTTGATGCAGTTGCAACATCATTGCAGTCATTTGTGGAAACCTGTGCAATAGCCTCTTCATGAACAGGGGGCATGTTTTTTTCATTTATTGCAGAAGTTGTGCTTTGATGCTGGGTCTGGGATTCTTCTGCACTTTCAAGTTTAAGTCTTTCCTTGGATTCTTCTGCACTTTCAAGCTTAAGTAACTCATGCAAACTTATTTTCTTCTCACTGATATCACTAGCAGTATCCCTGCTTTCAAGATCACATTGTTTCTCCGTGTTATCGTCAGCAGCGAATCCAACAGGTAGGAGAACAGTTTTTGGTTTCTGTCCATGTGCATATTTTTTAGCATCACCTTTCCCCCCATATGTTAGATCACTATTCGTGTCTATCATTAGGAAATCAAAATTTGGTGGTGACTTCTCATCTAACTTTTTTTCTGCTGAAATTTTCCGATGCGGAAGTACTCCTTCATCGATGCAGACATCCTTGACAAAATTGCCACCATAATCAGAAGTAACAACAGTATCTGGCAATTTTATCTCCAAAACATCCTTGTCGTAAGAAACATCATCATGTACTACATGTCCAGTTATATCTATCATATCTTGTGTTGGATTTGAGGCTTCTACCATTTTCCCTATCAAAACCCAGCCAATCACTTTTCTCGTATACTTCTGTGTCCAGTTTCAGTCTTTCAGACCAAATGTAGCTATCAAGCTACCTCCATCAGAAATTTCACCGTTGTCAAAATTTTCATCATCTACTGTGAGTAGACAAGGGTGCAACTGAAAAGGTCACCTAGTTTCACGATATAGATGCAGATCTTATGGAGAAAAGAATTGCTTATGTCCTCAAGTTCAGATAAACTCGGCAACTAATTCTCTTCTCCTACCTCCTCTTCCAAAATCGAAAGAAACGTCAAGGAGAGAGTTTGCAAGCAGCAGAGGGAGAAGGAAGGTATGAGTGAGCCTACGGGGGATCGCAGGAAGCCTAATGAACAAGGAATTCGGAAGTGAAGGAGAAAAAAAAAATCTGAACGGAAGCATGGACACTTAAATAAAAGGCATGAGGGCGCAGAGCTGTGCAATAAATTCGATCGATGCTCTCTCTCTCTCTCTCCTCCCTCTTCCCTCCCTCTCT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.918947
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0170500.1 2 22438595 A G
Osa02LNT0170500.1 2 22439022 A G
Osa02LNT0170500.1 2 22440163 G A
Osa02LNT0170500.1 2 22438096 T C
Osa02LNT0170500.1 2 22440194 A G
Osa02LNT0170500.1 2 22436549 C A
Osa02LNT0170500.1 2 22436897 A C
Osa02LNT0170500.1 2 22437195 C 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
Osa02LNT0170500.1 osa-miR5532 Translation 5.0 14.469 1 22
Osa02LNT0170500.1 osa-miR6253 Cleavage 4.5 6.839 1 22
Osa02LNT0170500.1 osa-miR818f Cleavage 5.0 10.936 1 21
Osa02LNT0170500.1 osa-miR167e-3p Cleavage 4.5 21.545 1 21
Osa02LNT0170500.1 osa-miR167i-3p Cleavage 4.5 21.545 1 21
Osa02LNT0170500.1 osa-miR1429-3p Cleavage 4.5 19.162 1 21
Osa02LNT0170500.1 osa-miR1850.2 Cleavage 5.0 11.571 1 21
Osa02LNT0170500.1 osa-miR2919 Cleavage 3.0 12.208 1 19
Osa02LNT0170500.1 osa-miR5515 Translation 3.5 23.442 1 21
Osa02LNT0170500.1 osa-miR5524 Cleavage 5.0 13.211 1 21
Osa02LNT0170500.1 osa-miR2919 Translation 4.0 24.962 1 19
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0170500.1 2 yld2.1 Morphological trait Seed RM262 RM263
Osa02LNT0170500.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0170500.1 2 qCSH2 Resistance or Tolerance Cold tolerance RM262 RM263
Osa02LNT0170500.1 2 nan Resistance or Tolerance Insect resistance RG157 RZ318
Osa02LNT0170500.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0170500.1 2 qRTT2-1 Resistance or Tolerance Drought tolerance RG157 RZ318
Osa02LNT0170500.1 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