Sequence
atgc intronic sequence ATGC exonic sequencegtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTCCGCGTGCGATCGAGTAGATCAAAAGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCGGTTCGTCTCTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G134613_T07 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------gtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTC------CGCGTGCGATCGAGTAGATCAAA--AGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCGGTTCGTCTCTC
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gtaagtcttctccgcccctagctgtcgatcgatcgatagattattcgattatacgatcgccgaatttggtggtgttcttttttttttttttgggtctactcgtcgatctgagccgtgagggtttgttgcga-gattgg-cgtgctgtgttgtggggtggtgttgattttttgtgtttgtttgcagGAAAGGTAGTAGTGAAGAAAGCAAGGCAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTCCGCGTGCGATCGAGTAGATCAAAAGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCGGTTCGTCTCTC
ccctgac putative branch site (score: 3)
ccccgattttttttct putative PPT
attttttttctgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcgccggccaccgtcaatcgattcgatttgatcgttccccttccccgcgcctcctcgttcccctgaccagtcgccccgattttttttctgttccagGTCGCTTCTCTCTGTTCCGCGTGCGATCGAGTAGATCAAAAGGAGGAGGAGGATGGCGAGGAGTTCGTTCAAGTTGGAGCACCCCTTCGGTTCGTCTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA