Sequence
atgc intronic sequence ATGC exonic sequence...tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattt-tgatccaactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
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--------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG
upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 3
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
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------------------gtttaagcaacttcttaaa---gttca--tctttgtttgtgttgtgttatggtgttgactgtatttggt-tgttt-----agGTTGTTGACTGTCGTATATGTGGTGATCCCAACTCAGTACTTAGGTTTGCTTTCATCGAGTTCACTGATGAAG
upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
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-------gttgaaaatattttcttgaagctct---catctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
ttttgat putative branch site (score: 4)
tgctctct putative PPT
atttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-gtacaaa
- - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcata