Sequence
atgc intronic sequence ATGC exonic sequencegtaaggattacgctcgaggctgctccacgattttcgtatgttcccttttgccggtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------gtaaggattacgctcgaggctgctccacgattttcgtatgttcccttttgccggtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA--------------
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gtaaacgcgcgaagctctgaatccatcctctgttcctcgcggtctcgcgtgcgtgccgtgctgcttgctggttgatgctaatctcctc--actcgcgtttcgcctgt--ttgttgttgcagATCATCCCGAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCCAAG
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 1
gtaaggat-tacgctcgaggc-----tgctccacgattttcgtatgttcccttttgccggtgttaatactgta-------tttgctaccgc-agATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA--------------
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gtacgcatctgagcccaaaatcaatgtgtcccgtcggttcaattcgttggtgaatactggcgctgatgttgtggtgtttttttttttctgttagATCATCCCCAAGAAGAACCGGAATGAGATCTGCAAGTACCTCTTCCAAG
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G37470.1 (Glycine max), 3'ss of exon 1
------------------------gtaaggattacgctcgaggctgctccacgattt---tcgtatgttcccttttgcc--ggtgttaatact-------gtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA--------------
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gtacgtcgtcaatttcttactcgtttggaatttaatctcgattcctttgcatcgtttcgttcattttttttttttcactctgatgcaaacatttgcgtgcgtgtttatttgttcagATCATCCCGGAGAAGAACCGCAAGGAGATCTGCAAATACCTCTTCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgattttcgtatgttcccttttgccggtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA
tgttaat putative branch site (score: 3)
ttaatactgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggattacgctcgaggctgctccacgattttcgtatgttcccttttgccggtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC