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

>Osa02LNT0164800.1

GACGCAAAAGACCCAGCAATAAGTATAGTTACATCCACTGAATTATGCTACATTAGTTGCAATTCTTAGATGCTGTAATCAACAGCATAAATAAAGTGTGTACGGTGCCTCCTCTACATTAATATCATATACACAACGATGAGGTCATAGGCAAAATCAGGATCCCTGGCACAGGCCAAGATGGAAACAAACTTACCATGCAAACGTCAGACTTGTCAACTGTTGAACTCCTCTCTTCAGCTCGACTTGGCAAGCATCCTAGCCGAATATGAACTGCAAGCACATTGGCTGGTAGAGCAAAAGGCAGGCTTTGCGATAGTAATGTTAAAAATGATCCAAGAACCGCGTCTCTTCAGTCAAAGATCTCCTGGGCTTCGATTTTGCTGTGCTGGTGTTCATCCTTGGAGACTCGGTAGTATTTCTCGGCGAGCTGCCTCTGACCAATAAGCTGAGCAAACCTCTCGTCATGGGTGATCACAATCAACTGGAAGTTCTCCTGCCCTTTCCTGCTCTCCATTATTCTCAAAAGGGCACCAGCAAGGCTCTCTGCATTAGGCCCATCTAGATTGGTGGTCGGCTCATCTAGAGCTAATATGCCACAGTTCAGACAGAATGTTTCTGCCAGTGCCAGTCTGATTATAAGCGACGCAAGCACCTTCTGGCCGGCACTGCAGCGCCCTCGCATTTCCAGCTCAGCATCACCTGTTTGCATGACAACACGATAGCTGTATGATCGAGTGCCAGCACCCTCAGAGTCAGAATTAATGCTTATATAGTCGATATCTTGGCCCCTATATGTCTGTTGCCACAGTTCCTTGATTATTTTGTTTATCTCCTCCATTTTCATGGTGTGGAACCGCATAAGAGCCTTATCCAAAGCAGCATAGTATCGGTCCAAGTCCTTGTTTGCCATCTCAGTTGTCTTTAGTTGAAGAAGTTGGTTAAAGTATCGCTTCTCAATATCCTTGTACTGCGTCTGTTTAAGTTCAAGCTTGTGTTTTGAAATATTACTTTGATAAACGGACTGCGTTCCTTGACACCTATTATACTCTGAAAGAAGCCTATCTTTTTCTTGTGAATGTTGCTTAAGATCCGCTTCTATAGTAGACAGGCTGCCAATGGAAAGTATTTTGTCCTCAAGTAATTCTATTTCATGAGTAAGTCGTTCCACTTCATCCTTTGTTCTCCTGTAGTTAAGGTTGTCATCAATGTTTCTTTTCAACTGATCTTGGCTCTTCAATAGCTCTTTGTTCTTGCTTAACTCCGCCGATTTTTCTTCTTTTCTTTCCTTACTTTTCTGTAGATCAGACTGCAACTGAGTATGTTTTTCCTGTAGTTCATTAAGCTTCTCGCCCTTCTTTGAATTCAGGTACCCTTTGATACGCTCATTGTGTGTCTCGAGTGCATCAATTTCCTGCTGGAATTCCCTTTTTCTTTCTGCCAGCTGATGATACTCCTGATCAAGCTTTTCCTTCAAAGCTTCATGCTCTTGCAACAAGCTTTCTCTCTCTTTTGACAACGGACCAAGAGACTCCTCTAAATGCTTCTCTTCTAATGTTAGTTTTTCTTTCTCCTCAGCTAGATGTCCCAAATCCTCTTCAGCTTTTTGAAATTTGTGCACTGCACCTGAAGCTTTTAGCTTCTCTTCCCTAATATCATGCCATCGCATCTGAGCATTAGTCAGACCATCGGTAAGTGTTCTTTGTTGATCCCTTAGATCATCCACTTCATTGTTCAATGTGTCCCTTGTCCTCTGCACAGAGTTCAACTCCAACTGGATTTGCTCCAAAGATTTAACACCTTGGCCACGAACATCAAGCTTATATTCAAGATTTTCAACTTGTGGTCCTAACTGCTGTATTTCTTGTACGTGCCTATCAATCGTTTCAACTGGCTGTAGCAATACCTGCACTGCATCCTTGTCCATTTTAACTTGAGCAAGAACACTGACAAAATCATCAAATGTTTGTGCCTTCTCACTTTCATCCGCCAAAAGTTGTTTCAAGTTCTTCTCTGCTAGAGGTATAGCCTCTTTTCCCAGCTTCACAAATTCCTCATAAGTTGCATTGAGTTTATTCAATTGCTGGAAAAAGTCTTCAGCATTTGAGCATTCCAATGAGATCTTGTTCATGCGATCTGCAGTACTTTCACACGTTGTCCTTTGCTTCTTTACAAATTCATCCTCTTCATCAGGTGTGAAAGCACGTTGACAGCAAGGGCACATGTGGAGCTCACGAGCCAAATTTTCAAAAGGCTCATACATTTGCCGCATTCCCTTCGCGTAACTTAAATTGTTTTTTTGTTTCTCTCTTTCATCCATGGCATCTTTCAGATGTTTGGGAAACATGTTAATGTCAGCAGACATCTTCGTAATGGATTGAAGTTTGGACTCCACATAGCTTCTCTTTGCATCCAATTCCTTTTGAAGCTTTGACAAGTGGCTCCTAGCATCAAGTATTTTCATCTGTACCAGTTTCAGCTCTTGCGCTGCTTCCTGGGATTTTGAGTTCAAATCATTGTATTCTCTGTCTACAGACCCAAAGGCTTGACTAAGTTCCTTCTTGACTTCCTTCTCAGAAGGAGTCCTCCCTTTAAACACAATTCTGATTTTGTCCTTATGCTCATCAAATATCTTTTTAAGTTTCTTCTTGCTTTCTTCCAATTCATCCTTCTTCACGTCTAGTAGTACCCTGTCATTGGAATCACTAATAATGCTGTCTTTTTCCCACTGAAGTGTTTTTATCTTCTGGTCCAAGCTAAATATCTCTGTGCGCTTCTGATTTACAATTGAATCATAGTTCCTTTCTCCCAGCGCAAGTGCTTTCCTTTCAACTTCAATTTGCAGATGTCTCTCCTTTTCATCAATACGGGGAAGATTGTACTTTGAAAGGTCCATTTCCGCGGCATCGCGTTCACTCTCTTTATCTTTCATGCGCCTTGAAATACCTTTCTTGGAGGCAACCTTAGATTCTATCTGGCCAACAACTTCAGAGTAGCGAGTATTTACTTCAAGATAGCGTCCCCACAGAAACTGTTTCTGTGCCTCATTAGATTTCTTCTTATCCTGCAAATCATCATTAAGATTTGACAGTTTTGCTTTAGTTATGTTTGTAAGGTGCATGGCAGCAGCATCAGTTAAAGGAGCATCAGGTATTGGCCCAAGATTATGTTTGGTGAAGATCTTTCTGATTGCTGAATCCCGTTCGTGTTTCACTGACATGTGAGCGTCAGCTTCTGCCTGGAGCCTTCCTGTTTCTCGCATCAAATCATTTATGGCCTTGGAAAGGAAGGAGCTTGTTGTATTTTCATCATCCACATCTCTTTCTAGTTTACTGATCTTATTTTGCAGCAATGCCATTCTTTCTTCAAATTTCGTTTGCCACTCCTTTAGTTCATCATCGGTATCTTCGTTTTCCTCAGAAAGAGCAGCATACTGTTGCTGCTGAAGTGTAAAATATGTAGTTCTAGCAGATGTACTGGAGTTAATTTCCTGTTGAAGCCTCCTCAAGTCAGCTAAACTTTTTTCAGTACGACGAATTTTGTCTTCAACACCTTGAACGTTTGTTCTCAGTTCCTCCATTTGAATTTTTAAGGCATCTGACTTCTCTTGATCTTGAGCAATATTGTCACGGAGCCTATATGCTTGGTCTTTTAGAGTCTGAAGGTTCTCCAACTTTAACCTAAAAGTCTTGATTTCCTGTGCTTGATCCTTGTGAAGTTTTTTTATGACTTCGAGAGCTTTGGTATAGCGGGTCGCAGAAAAGATATCGTCAAACTTCTTCTTAAGTGTCGATGGATCCTGCAAAGGCCAATTGGACTCATCTTGGTGCACGAATATAACATTCTCCAGTATAGCCTTTGATACACCCAT

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.837603
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa02LNT0164800.1 2 17490969 C G
Osa02LNT0164800.1 2 17490071 A T
Osa02LNT0164800.1 2 17490923 T C
Osa02LNT0164800.1 2 17491825 G A
Osa02LNT0164800.1 2 17492232 A G
Osa02LNT0164800.1 2 17492338 T C
Osa02LNT0164800.1 2 17493488 T G
Osa02LNT0164800.1 2 17493634 T C
Osa02LNT0164800.1 2 17494047 G T
Osa02LNT0164800.1 2 17494649 A G
Osa02LNT0164800.1 2 17494659 G A
Osa02LNT0164800.1 2 17495678 G A
Osa02LNT0164800.1 2 17495920 T G
Osa02LNT0164800.1 2 17496265 T G
Osa02LNT0164800.1 2 17496831 A C
Osa02LNT0164800.1 2 17498307 A C
Osa02LNT0164800.1 2 17498985 G A
Osa02LNT0164800.1 2 17499096 A G
Osa02LNT0164800.1 2 17499184 A G
Osa02LNT0164800.1 2 17499536 C T
Osa02LNT0164800.1 2 17499626 T C
Osa02LNT0164800.1 2 17499964 G A
Osa02LNT0164800.1 2 17500122 A G
Osa02LNT0164800.1 2 17500134 T C
Osa02LNT0164800.1 2 17500247 T G
Osa02LNT0164800.1 2 17500797 A G
Osa02LNT0164800.1 2 17501863 A T
Osa02LNT0164800.1 2 17502161 T G
Osa02LNT0164800.1 2 17502676 C A
Osa02LNT0164800.1 2 17503613 T C
Osa02LNT0164800.1 2 17504303 A T
Osa02LNT0164800.1 2 17504539 T C
Osa02LNT0164800.1 2 17504759 T C
Osa02LNT0164800.1 2 17502565 G T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa02LNT0164800.1 DTM_#DNAt_MULE_japo_Os2081 Chr2 - 17495073 17495433 360
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa02LNT0164800.1 osa-miR5537 Cleavage 5.0 15.603 1 22
Osa02LNT0164800.1 osa-miR5793 Cleavage 5.0 13.766 1 21
Osa02LNT0164800.1 osa-miR5798 Cleavage 4.5 16.199 1 21
Osa02LNT0164800.1 osa-miR5817 Cleavage 5.0 15.214 1 24
Osa02LNT0164800.1 osa-miR5830 Translation 4.0 13.563 1 24
Osa02LNT0164800.1 osa-miR1440b Translation 4.0 9.502 1 21
Osa02LNT0164800.1 osa-miR1440b Translation 5.0 14.522 1 21
Osa02LNT0164800.1 osa-miR6252 Cleavage 3.5 11.826 1 23
Osa02LNT0164800.1 osa-miR6252 Translation 4.5 13.174 1 23
Osa02LNT0164800.1 osa-miR6255 Cleavage 5.0 13.798 1 22
Osa02LNT0164800.1 osa-miR395u Cleavage 3.5 15.483 1 21
Osa02LNT0164800.1 osa-miR395u Cleavage 5.0 10.152 1 21
Osa02LNT0164800.1 osa-miR156k Cleavage 4.5 14.43 1 21
Osa02LNT0164800.1 osa-miR172c Cleavage 4.5 13.377 1 21
Osa02LNT0164800.1 osa-miR415 Translation 4.0 16.8 1 21
Osa02LNT0164800.1 osa-miR395w Cleavage 4.5 10.152 1 22
Osa02LNT0164800.1 osa-miR1426 Cleavage 3.0 13.377 1 21
Osa02LNT0164800.1 osa-miR2905 Cleavage 3.5 21.067 1 21
Osa02LNT0164800.1 osa-miR2873a Cleavage 4.5 12.727 1 24
Osa02LNT0164800.1 osa-miR2921 Translation 2.5 9.925 1 24
Osa02LNT0164800.1 osa-miR2921 Cleavage 5.0 14.478 1 24
Osa02LNT0164800.1 osa-miR395x Cleavage 5.0 18.093 1 21
Osa02LNT0164800.1 osa-miR5147 Translation 5.0 9.551 1 21
Osa02LNT0164800.1 osa-miR5340 Translation 2.5 16.48 1 23
Osa02LNT0164800.1 osa-miR5340 Cleavage 5.0 12.534 1 23
Osa02LNT0164800.1 osa-miR2275c Cleavage 3.5 4.199 1 23
Osa02LNT0164800.1 osa-miR5523 Cleavage 5.0 19.139 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa02LNT0164800.1 2 qPH-2 Morphological trait Dwarf RG324 RG83
Osa02LNT0164800.1 2 np2.2 Morphological trait Culm/leaf RM324 RM262
Osa02LNT0164800.1 2 qSS-2 Physiological trait Sterility RM301 RM263
Osa02LNT0164800.1 2 nan Resistance or Tolerance Drought tolerance RG83 RG171
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