Sequence
atgc intronic sequence ATGC exonic sequence...atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttcaattgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g36090.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 11
-atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttca------attgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
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aacaaacagtgtcaacagt-----aacatcttatttttcgtttttaa--agtaaaactacacattacaatttatcaagctaacatgtacatgtctcaatggttgcagCAATTTGTGGATGAAGTTATGGAACTAGTGGAACTCAACAATCTGAGCGACGCTATAGTTGGGCTACCAGGAATCACAGGGCTTTCAACAGAGCAAAGAA
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 15
atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttcaat-------tgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
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---agacatataacagatatgagaacaaacagtgccaacaataacatcttt----tttgtttttacaagttttcaagctaacatgtaacatgtctcaatggttgcagCAATTTGTGGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAGGGATGCCTTAGTTGGGCTACCAGGAATCACAGGGCTTTCGACAGAGCAAAGAA
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 14
------atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttcaattgt----ttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
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gtaatgagttggaacttagaactagtatagcttcttctaaattgattatgaggtagtcattttgagtgctaaaagtttttttttttttttttttttttttgctctttcagATTTTTGTAGATGAAGTGATGGAACTGGTTGAGATGGACAACCTCAAGGATGCCATAGTTGGGCTTCCAGGAATCACAGGTTTATCAACAGAACAGAGGA
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv09s0002g03560.t01 (Vitis vinifera), 3'ss of exon 5
------atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttcaattgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
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gtaatgagttggaacttagaactagtatagcttcttctaaattgattatgaggtagtcattttgagtgctaaaagttttttt-ttttttttttttttttctttcagATTTTTGTAGATGAAGTGATGGAACTGGTTGAGCTGGACAACCTCAAGGATGCCATAGTTGGGCTTCCAGGAATCACAGGTTTATCAACAGAACAGAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attactaggatttgtcgtcacaatttgtcaaactcacaagttcaattgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
aactcac putative branch site (score: 2)
ttgtttcc putative PPT
aattgttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaggtgttttaattttttgtgaatattgggtggttaatttctgattactaggatttgtcgtcacaatttgtcaaactcacaagttcaattgtttccagCAATTTGTTGATGAAGTTATGGAACTAGTGGAGCTCGACAATCTGAAGGATGCGTTAGTTGGCCTGCCTGGAATCACAGGGCTTTCAACAGAGCAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG