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

>Osa03LNT0230500.1

GAAACAAAAACTCAACCATGTATAACACTACTTATTCCTTACAATCAGTAAACATCCTGGTAAAATATATCATAGCGAAGTCTTAAGAGAGACTAGAAAGAATATAAGGGAGCATATCTACCGACGCTTATCTCGACTGCGTAGGGGAGCAGAGGAGGCCTGAAGCATCTGCACCAACCACGGCAAGCTCACATATGGTACAAAGCTGCCCTTCGATCGAAGGAACAAACCGGGAGCCACAGTACGGGCAGGAAACATCCTTCTGGCCACGGTAGATTGGAACATACGTGGCGCCACAGACAACAAATGGATTTCTGTAGTCATAGTTCAGCTCAGAGCTATCCTTCTTGCCACTGCACTGCTGCTGCACCTGTCGAGCCCTCCTTGCTTGGGCCTCATTAGGGTTGTTCTCCAGAAGCATCCTTGCAAAGTGCTCTGCAGTAGCGAAGTTCTTTTGCTTGTAGCACAGACCCATAGCGCTTCCAAGCACAAGCCTCATATGAACTCTCTGAAGCTTGCAGTTAGTGAAGTAAGCCGCCAATTCTTGTTGGCGGTTGACATCATCTCTCAGCTCCTTCCTCTTAAGTTCCATCCTCAGGCCAAGAACATACTCCCTCACAATCTCGATCAACTCTTTCACTTCATCCACTTCCCTCCTCGAGTCTACCACGATAAGAGGGATGGTATGCAAGATGCTAAGGAACTGCCTCAGGGCTTCTGGGAACTTACCATCTGTGGTGGCCTTATAGGCAGCCTTGAGTCTGTCTTCCATTTGTGGGAAGGTGAAAACAAGTGCAGGAGGGCCTCTCACGTTAGGACTTGCAGACTCGCTCCAACCTTTCTCAACAGCGATTGGTATTATGGGGGCAGTTGCAAGTGCACGAAGATATGAGTGGCTGCCCATGTGCAGATCAACAAACAGGGGCTTGAGGGGAGCAAAGTTTTTTATGCCCAACTGGCGGCTAAGCAACCTCATTGCAGTGTCAAAGTTCCCTGCTGCGGCATGCTCCCCAGCAAGAGAAGATTTCTGAGTCCAAATCAGGCTGACAGGCATGCCTGGTGGAGGAGCAACGAAGACCGCTGAGCGTGCATTGCCAGCATTTTTAGGGGTCTCTGCTTCAGGCGGAAGTTCCAGATCTTCTAGGTCCCAACCACCTTCCTCGCCATCCTCCTCATTTGCTTCACCCTCCTCAGCATCAAAACCGTCACCACCATTTGCCATCGCTTCGCTTGCATCAACCATATCCAGGTCCTCATCACCCCAGTCAGCACCAGCAGCTTCATCGTCTTCCTCAAGTTCAGCCTTCCCAGTAGCATCCAGTCCACCCTCAAAGATACCATGCATCACCCTAAGCAATGGCCAATCACCACTGGCTGTAAGAGGAGCAGGGGGGATCAAAAGAGAGCGAGCTTTTCCTTCAGGAAGAGAAGGAATATTTTCACCCAGCTCAGCGGCAAGCCTATCAGCAATTTCTGTGAGCCCATGGGTGGTAGCAGTAATATAAGCAAGAGGTAGCTGTCCAGCATTCTCTAGGATCTCAACTCTCTTCAACGCATCACCAAGATACAGAGCATTGTGGAATTGACCCATCAGGTTATTGTTCTGTCCAGCAATTTTGCACATGAAACCCACCTTGTCCATGTAACCAGTAATAAGATATAGGAAAGCAAGCCTCTCAAAATTCTTCGTACGTTGGTATGCATATTCCACAATACCAACATTTCCCTGCCTCAGGGCCTCAATTCCCAACCTGTACCAGTGATCCTTGTCATCAATCTCTTTTGCAGAAGCAACTGCGATTTGGATGTTACCACTCTCAAGAGCAAGGTTAAATCTTGTCTTCTCATCTTTCACAAAGTGGAGGGCAACTTCTGGAAAGCCTTTCTGTTGTAAATAAGAAATCACAGCTTGCCCACACAGCTGGGAATTCTTGATCATACTCATCACATGATCATACCGTTTGCGTAGAAGGGCCAGCTTGAAAATGTACTCAGATGCATCAACTGTGACCAGCTTGTTCTTACCATCACGATCTAGACAGAATATATTGTTCCCAATAACCCTTGTTATGTATATAGGAACATCGAGGGTTTTAATAATCCCACTATCTCCATTGGGAAGGCAATACTTGATATGATTCAGGGTAGTGTAAATAAACACACCATTCTCATCCCAGGCACCACTTTTCACACGAATGGTTTCGTGCAGTGTACAGCGATGGACGAGCTTCTTGTTTGCTATAACCACTGCATGCTTGCTCAGCAGTGCGACAGATTCCATATCACTAGACCAAACAACATATTTAACAGAAGGTGCCTGGAGCTCACCAAGAATTAACCTTTGCTGCAGATCAAAGATGGTCACTCGGTCTTCGGCTTTGCACAGCAAGTTACCAGTCCCAGCATAATAAATTGCATCCGTGGCAATAGGAAGAGGGCTTTTCTTTACGATTTCATTCTTAAGATTCTTCACCAAAACTTGATTGCTACTCTTCTCAAGGACTGCAAACCTGTTGCGTGCCACGAAAACAGCTGACCCACCAGCTCCCTTCTTTGCATCCTGCAAATAGTCAGCCCTGCCAGCAGAATCCTTGGGAACAATGTAGAGTTCGTATGAGCCTCCATCCACATCAGAGCAAATCAGGACAGCATTTTCAGTTGGACTGTAAGATAGTGTCTTGGGTGACTGGTTCAAGCTCACTGATCCAGGTCTTCTTATTGGAGCAAGCTGAACTTCCTTCTGTGTGGTGAATTCAAAAAAACGAAGAAAACGGTCCTTCACATAGAAAACAGTATCTCCACTCACAGAGAAAGCTGGACGTTCCCTCTCCAATTTAAACACAATCATACCACTGTCATGACCAGCGGCAAGAAGATTCATCTCAGGGTGAGCAGAAAGAATCCAGAAACGATCATGTTCCCGCCTGAACGTTTGAATACCGGTTCGCTTTGTGGCATCCCAGATGCGAATGCTTTTGTCCTCTGAGTTGGACACAATGATGTCTTGCTTAGCATGGAACATCACGCATGACACATTATTCATGTGTCCCCGCAAAGTATCAACTTCCCAAGCCTTCGTGTCATTCATTCTCCATAGCTTCACTTGTCGGTCATCTGCCCCGGAAACAATGAGTGGCAATGTGGGGTGAAATGATGCCCAGTTCACCCCACGGTCATGCCCTTCCAACACATATTTTACAACTGCATCAACACCTCCAAACAGATCTGTGTTCATCTGGGTGAGACGCAGGATGTCATCTGCAGGTGACACCGTCTTCTTCCTCAAAGCACCAATATCCCAAACACGGACAGTCTGATCCAGTGATGCTGACACAACCAGGTCCTCCTTGGGATGGAATGATGCGCACATGACATAGTGGTTATGTCCAGTCAGCACAGCTACACATGTGCGTGACTGCCAGTTCCAGATCCGGATTGTCTGGTCATCACTAGCACTTACTATCCATGGGTATTCGTGGTGGAATTGCACGGTGCGAATATAGTCAAGGTGCCCGTGAAGTGTGAAGAGGCAGCGGTGTGTCTTGTAATTCCACACCTTAATCTTGTAATCATCACCTCCGGAGACGAAGAGCGGCTGCGTGGCGTGGAAGTGGACGCCGCGGACGGGGCCGTCGTGCTCGTCGAAGCGGTCGAGGAGGGTGCCCATGCGGTAGTCCCACATCTGGATCACCCCGCTGTGGAGGCTGGCCAGGATCCATGGCCGCCGCGGGTGGAAGCTCAGCCCCTTCACCCGGTTGCTCTTCGTCTCGAACTTGGTCAGCATCTTCGCTTGGCCCTCCCGCCCCTGATCGTCGTCTCCGGCGACGGCGGGCGCGGCGGCGGAGGCGAACCCCTAGCCCCGGAGGCGGAGACGAGCGGAGGAGAGGGGAGGCGCTGGATCTGGGGCGGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.613037
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa03LNT0230500.1 3 28719905 G C
Osa03LNT0230500.1 3 28719974 T C
Osa03LNT0230500.1 3 28721789 T C
Osa03LNT0230500.1 3 28722485 A T
Osa03LNT0230500.1 3 28723055 C A
Osa03LNT0230500.1 3 28723127 A C
Osa03LNT0230500.1 3 28720561 A C
Osa03LNT0230500.1 3 28723760 A G
Osa03LNT0230500.1 3 28725143 C T
Osa03LNT0230500.1 3 28725152 A G
Osa03LNT0230500.1 3 28725172 T C
Osa03LNT0230500.1 3 28725229 T C
Osa03LNT0230500.1 3 28725275 T G
Osa03LNT0230500.1 3 28725825 A C
Osa03LNT0230500.1 3 28725837 A G
Osa03LNT0230500.1 3 28726090 T G
Osa03LNT0230500.1 3 28726172 T G
Osa03LNT0230500.1 3 28726557 A G
Osa03LNT0230500.1 3 28726930 G A
Osa03LNT0230500.1 3 28727818 T C
Osa03LNT0230500.1 3 28728351 A T
Osa03LNT0230500.1 3 28728912 A C
Osa03LNT0230500.1 3 28729084 T C
Osa03LNT0230500.1 3 28729432 A G
Osa03LNT0230500.1 3 28729595 A G
Osa03LNT0230500.1 3 28729765 C T
Osa03LNT0230500.1 3 28729894 T C
Osa03LNT0230500.1 3 28730425 T C
Osa03LNT0230500.1 3 28730582 T C
Osa03LNT0230500.1 3 28731183 A G
Osa03LNT0230500.1 3 28731615 C A
Osa03LNT0230500.1 3 28731995 C G
Osa03LNT0230500.1 3 28732080 G T
Osa03LNT0230500.1 3 28732320 C A
Osa03LNT0230500.1 3 28732722 A G
Osa03LNT0230500.1 3 28733181 C T
Osa03LNT0230500.1 3 28734449 C T
Osa03LNT0230500.1 3 28729408 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa03LNT0230500.1 DTM_#DNAt_MULE_japo_Os0243 Chr3 - 28726985 28727760 775
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa03LNT0230500.1 osa-miR1440b Cleavage 5.0 13.699 1 21
Osa03LNT0230500.1 osa-miR319a-3p Cleavage 4.5 12.264 1 21
Osa03LNT0230500.1 osa-miR1431 Cleavage 5.0 17.912 1 21
Osa03LNT0230500.1 osa-miR1879 Cleavage 4.0 14.385 1 24
Osa03LNT0230500.1 osa-miR1846e Cleavage 5.0 19.333 1 20
Osa03LNT0230500.1 osa-miR2275a Translation 4.5 21.217 1 22
Osa03LNT0230500.1 osa-miR2275b Translation 4.5 21.217 1 22
Osa03LNT0230500.1 osa-miR2872 Cleavage 3.5 18.653 1 21
Osa03LNT0230500.1 osa-miR5490 Cleavage 5.0 18.491 1 21
Osa03LNT0230500.1 osa-miR5501 Cleavage 3.5 17.838 1 21
Osa03LNT0230500.1 osa-miR5507 Cleavage 4.5 11.899 1 21
Osa03LNT0230500.1 osa-miR530-5p Translation 3.0 20.971 1 20
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa03LNT0230500.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0230500.1 3 qRFWd3-2 Resistance or Tolerance Other soil stress tolerance C944 C746
Osa03LNT0230500.1 3 qRFWw3 Resistance or Tolerance Other soil stress tolerance C944 C746
Osa03LNT0230500.1 3 nan Resistance or Tolerance Drought tolerance C746 RZ448
Osa03LNT0230500.1 3 nan Morphological trait Shoot/Seedling RZ403 RZ630
Osa03LNT0230500.1 3 nan Morphological trait Shoot/Seedling RZ452 RZ448
Osa03LNT0230500.1 3 nan Morphological trait Panicle/flower RZ448 RZ403
Osa03LNT0230500.1 3 nan Resistance or Tolerance Blast resistance RM16 RM168
Osa03LNT0230500.1 3 Qpn3 Morphological trait Culm/leaf CDO337 OSR31
Osa03LNT0230500.1 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0230500.1 3 nan Resistance or Tolerance Drought tolerance C136 R1618
Osa03LNT0230500.1 3 qSV-3-1 Morphological trait Shoot/Seedling RM156 RM168
Osa03LNT0230500.1 3 Yd3-13 Morphological trait Seed RZ403 CDO337
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