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

>Osa01LNT0020400.1

ACCTATAGTAAAGTTCGTCACACATTTGAATCTATGGCGTGGAAGAGAATTTTATTTGATGAGCAATTAACGAAAGGACAACACCTATGACTAGAAAAGTTTTGCTATATGCCTAATTGTACTGAACATACGGTTGCTAGCTAGAATGTTTCTAAATGATTTCGAGGCTTTGAGCTATATACATCTTCAAATGAATTGAAGTCCCAATTTCAGTATATGCTAAATACTTGATGCATGTCCAGAGAAGAATCACATGGACGGTGTTACCTTTTCTATTCATAAATGTACACCTAAATCTTCCTGCTTCTCTTGTATTTGTATGTGTTGAACTTCAATCTCACCAGAAACTGAATTGGTGGGGAATGGATCTGAAAGGTTAACTTTTCTGAAAGCCAAGTAGATCAGAGCAGCAATATAGGCTGCCATGAAAGGGAAAACAAGGCTGCTAATTATTGCATTAACAACCCTTGGAAGGTCGCTATGAACAAGCCAAGCGACAAAGCTAGTACAGAAGAAATAAATATTGATTCCAATAATCACCAATGACAGTATCCACGCGATTCGGATAATCTACATAAAAGAGTAAAATTCCCAAGAGTTAAGAAGAATGAGTTCAATTTGATGACAAATGTATGCCATTTTAAGACAACACAGGGAATAATGAAAACTATGGTGTTATTGAGGAAGTAAAAGTTATTCTATGCAATAATGCAAATTATGTTGAAGATTTCCGATTATCTAGTAATTAAATGGAAATAATTCTTCAAGTAACTGTGATTCATTTGAAGTAAAACCATTGTCTAAAAATATGGATGCAGAATATAATAACACAACAAGAAACGTTACTACCTTGAAATTACTCTCACTCTAGAATTTGAACCATAATTATATACTCCAATGTTTACTGAAACACCATGCTATGAGGTAATTTTACAAATTGAAAGCTCTAACATAGTAACATGCATTCGTGATCAGCCTACAGTTCTAGTTGAGATTTCAAATCTCATATATTCACTCTTACAATGGGATATATGTAACGCCCATGTTCCAACATGCACATGAACCTAGACTTGATACACCAGAACTCTACACATGGATAGCCATATAGTAGTTCTTAGACTATCATAACAAAGTAATTAAATTATATGTTGCTACATTTGGTCCCTAGTTGATATAGTGTTTCATTCTAAGAGTATAACTATGAAAGAATTACCCATAAATCATTTTGATATGAATGAAAGACATAGATTTGCAAATATATTTCAACCATAGAGTATCAGACAGGGAAGAACCAACAATCACCACTGTCTACCAACTCCATTTTATGCAAATAAAGATATACCTGGCTGGAACTAGAATCTAACATTATTTTTTCTTTCTGTTGCCATCTATACACTAGCTCGTATTTGCACCCCTTTTCTAAAAAGCATTGGCATGTTATTAAGTGGAAAAATATATTATATATATATGAGAGATGCTAATTATTATTTATCCAATGATTTTATGGTTTACATGTTGGCACATAAAAATAGCAGCAGGGACATCAATTTATCAATAAGAGAAGCTGGGGAAATATTGTGTGTCAAACTCAATGCAAAGTGGACACTGAGGAAATGGGGGTATGTGCACAAAAGAAAAATGTTCATGAAAAGGGGACTATCATGCTTATAGCTTCTATTTACAACTGTTTAGAAAAGAGGAAAAGAGTCTGCTAATTAGTGTTTTTTCCCAGCACAAACTACTTTAGAGTTGTATAGTTACCAGTGGTAAGTAAGGCGTATAAGTTATTTACATATGTACAGCAATAGCTGGTCACAAAAGTGAAATGAATTGTGTAAGTGGCAGTGGGGAGGTTGAAGAAATTTGGTTGGTCAAGGCCAACCCACTGCACTGTATTCCTTTCCATGAGTGCTTATTTGCCCTTGGCACATTCACATGTTGAGCTTGGACCCACATGTAACTGAGAGAATGAGGGACGTGCATATCAACTTTTAGGGGCAAATAAGGTTCTAACATTTTGGTTTTTTATTGTTCCATCTGTAACTTTTAGATGCCCTGGTAAGAGTGTATCATACAATAATTTGTAGTGTACGATCCTACATACATCTAGCACAAAAATATCTTTTTTCTTAATTTACAATTATCCGCTAACATACATAAGGGCATTTAGATTTCTCGTAAAAGATATTTTTCATGTTATATATATATCATAAATTCTCTAGGACATAATTATACATACAAACTAAATGAAAGTTATGTAATGGAAATGGACTATGATCGTGTCCAAAATGACTAGTATAACCAAACAGATAGAGTATGTCATAAACAAATTGAATAGTAAAAACTGTTTTAGCAAGCTTACAGATGTTGCATTCTTGTATGGTCCTATATTTGTGCAGCTGCTACTGAATTTAATGAGTGGAATTAGAGCAAACGGCAGCACAAATGATAGTACAATCGCAGCTATGTTGATAATTCGATGCACTCGTAAAGTACCACCAATGCTGCAAATTATCAAACTAGGTAATAAGGTGAAACAAGGAGCAACAAGATATATGATGCACTTTCTCATTCCGGAGAAGCCCTGTAACAACATTTGGTAAATCTTGCATGAAGAAATTTAGGGAGGAAAAAAATACAGAAAATCCCCATTTGGATACTGATATGAAACTAGAGCTTGGCCAGATTTCTATCTATTACCAGTTGTAACTAAATATTTTAACACAGAAGTTACATTTCAATTTTTCTAAGCAAAGTTACATTTCAAATTCAGTAGGCATGCAATTAGCTCGAAATATTATTTGGTAATATTGAGATGATACATCTTCTGAAGGTATGTACTACTAGGTTTATCCTTGAGGCCCTAATCTAATCTACTCCAGTAATTAGGTAAATGTACCTGCATGATGTATTGGCCAGCATAACTCGTAGCCACCATGCAGCTCTGTCCAGAAACTAATAAGGCCACACCATACACAGTTGAACTTGATTTTCCCAAAATATTCTTGAGTAGTACATAAGTTGAATTCAATGTTAGACTGCTGCACGTGCTTGTGTCGGCAAATGAGAGATTGTTGGCACATATAGTACCAGATATTGATACAATAGCGACATTTACAAGTAGTGCAATGAACAGAGCTAATGCATTCTCAAGCAAGAAGAATGTAGAAGCATCCTTGCGTCCTTTGGAAGTATATGGCATTTTTCTCGTTAGCACCAAAGAAGAATGTAGGAAGAGATTATGCGGAACAACAAGAGAACCAAACATAGCAACCGCATCTGAAGTAGAATAATCCCCTTTGGGCCTTGGGATAAAAAGCCCCTCAATTACCCCACCAGCAGGAGGATTAACTTTGCCAAGTTCCATAAAAAAGCAAGTAGCCATCACCAACATAAGAACTGATATAGTGAACTCCATTTTCCGAGCCCCATATCCTTGTAACCCGAGAATTAGGAAAGTGCATGCCCCACATGCTAGGACACCGGCCCAGAAAGGGATGTGGAGTAGCATGTTGTAGGCTAAAGCAGTTCCTAAAACTCCTGGTATAGTGGCAGCAATAACACCAAGCTCTGCTAGTAACCATAGGCAGTACTTGACATACTTTGGATATTCACCCATGCACAACTCAGCGAGGTGCCTTCCTGTAATGATACCCAAATTTGCTGCCAATGATTGTACAGTCAACACAAATATGAACCCAAATAGGAGTACCCATAGCAACGAATATCTGTGGCTGGATCCAGCTACCAAATCAGTCTGCAAGTTACTAGGATCAAGGTATGCGATGGAGATAACAAATCCAGGACCAACATGTGCAAGAAATCTCTTCCAAGTGGGTGCCTGGACATCGCCGTGCAGACCGCCGTGTTGCCGCGACGGCGAAGCCCCTGCGGCTGCGGCGACCTCAATCTCAATCTCGTCCCCGCCACCGCCGCTGCCGCCACCGACGGCCGCGACCCTCCCGCTACCGTTCACCCTCCCGTGCTGCTGCTGCTGCTGCTCGTGCTCCCTCCCGATCTTCGCCCCCTCCTCCATTGCTCTGTCTCAGTAGCGCAACTAGTGGTGGTGGTGGTTGACCATTAACCTGAACCTGGC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.949627
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa01LNT0020400.1 1 17456083 T C
Osa01LNT0020400.1 1 17456293 G A
Osa01LNT0020400.1 1 17456609 T C
Osa01LNT0020400.1 1 17457356 C A
Osa01LNT0020400.1 1 17462563 A G
Osa01LNT0020400.1 1 17463385 C G
Osa01LNT0020400.1 1 17463459 A G
Osa01LNT0020400.1 1 17463759 T G
Osa01LNT0020400.1 1 17463993 G T
Osa01LNT0020400.1 1 17461872 T C
Osa01LNT0020400.1 1 17460055 T C
Osa01LNT0020400.1 1 17460315 C T
Osa01LNT0020400.1 1 17460580 G A
Osa01LNT0020400.1 1 17460587 A G
Osa01LNT0020400.1 1 17460617 C T
Osa01LNT0020400.1 1 17460976 A T
Osa01LNT0020400.1 1 17461137 A C
Osa01LNT0020400.1 1 17454369 T G
Osa01LNT0020400.1 1 17454831 C A
Osa01LNT0020400.1 1 17458093 T C
Osa01LNT0020400.1 1 17458668 T C
Osa01LNT0020400.1 1 17459259 T C
Osa01LNT0020400.1 1 17459557 A T
Osa01LNT0020400.1 1 17460193 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa01LNT0020400.1 DTM_#DNAt_MULE_japo_Os0222 Chr1 - 17459615 17461154 1539
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa01LNT0020400.1 osa-miR5543 Cleavage 4.5 13.365 1 21
Osa01LNT0020400.1 osa-miR5788 Cleavage 4.5 8.52 1 21
Osa01LNT0020400.1 osa-miR5821 Cleavage 4.0 12.714 1 21
Osa01LNT0020400.1 osa-miR6248 Cleavage 3.5 14.453 1 21
Osa01LNT0020400.1 osa-miR6251 Translation 5.0 16.396 1 21
Osa01LNT0020400.1 osa-miR167a-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167b Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167c-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167d-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167e-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167f Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167g Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167h-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR167h-3p Translation 4.0 13.8 1 21
Osa01LNT0020400.1 osa-miR167i-5p Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR171f-5p Translation 5.0 24.874 1 21
Osa01LNT0020400.1 osa-miR167j Translation 4.5 14.807 1 21
Osa01LNT0020400.1 osa-miR820a Translation 5.0 16.242 1 21
Osa01LNT0020400.1 osa-miR820b Translation 5.0 16.242 1 21
Osa01LNT0020400.1 osa-miR820c Translation 5.0 16.242 1 21
Osa01LNT0020400.1 osa-miR1438 Cleavage 4.5 13.137 1 22
Osa01LNT0020400.1 osa-miR1863a Translation 4.5 13.705 1 24
Osa01LNT0020400.1 osa-miR2864.1 Translation 5.0 11.821 1 21
Osa01LNT0020400.1 osa-miR2920 Translation 5.0 21.578 1 23
Osa01LNT0020400.1 osa-miR812o-5p Cleavage 5.0 21.378 1 21
Osa01LNT0020400.1 osa-miR5485 Cleavage 5.0 12.455 1 21
Osa01LNT0020400.1 osa-miR5487 Translation 4.5 19.587 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa01LNT0020400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0020400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 R886
Osa01LNT0020400.1 1 nan Resistance or Tolerance Salinity tolerance RM1 RM5
Osa01LNT0020400.1 1 qNVB-1-1 Morphological trait Culm/leaf R2159 C178
Osa01LNT0020400.1 1 nan Physiological trait Source activity RG532 RM472
Osa01LNT0020400.1 1 brt1d Resistance or Tolerance Drought tolerance C742 C904
Osa01LNT0020400.1 1 rfw1b Resistance or Tolerance Drought tolerance C813 C955
Osa01LNT0020400.1 1 nan Morphological trait Root RM23 RM306
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