Sequence
atgc intronic sequence ATGC exonic sequencegtatgctacatgcttctaattaacatatgtttctctgtgctcgaagatgaaggtcatcatgatttatgggcttgtttttgtttttgttcctggattgtctaatattcataacgacttttgtttacttcagCGCCTAGATTGGAGTTCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 5
gtatgctaca--tgcttctaattaacatatgtttctctg-tgctcgaagatgaaggtcatcatgatttatgggcttgtttttgtttttgttcctggattgtctaatatt---cataacgacttttgtttacttcagCGCCTAGATTGGAGTTCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
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gtatggtatagttccttctaatttttatacgtacaccagatacttgaagttgaaagtgataatgat----gatttcatatctgtttctgttgttagagtttaatatatttactatgactactcatgttcactttagCGCCTAGACTGGAGTTCTAGCTCGTCTGCATCTTCATCGAAGGACTGCATTCTCCTTGCGGCCTGTGAGGCACATCAAACTCTCCCACAGAGCGCAGAAT
upper sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 4
gtatgctaca--tgcttctaattaacatatgtttctctg-tgctcgaagatgaaggtcatcatgatttatgggcttgtttttgtttttgttcctggattgtctaatat-----tcataacgacttttgtttacttcagCGCCTAGATTGGAGTTCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
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gtatggtatagttccttctaatttttatacgtacgccagatacttgaagttgaaagtgataatgat----gatttcctatctgtttctattgttagactgtttaatatattcactatgactactcatgttcactttagCGCCTAGACTGGAGTTCTAGCTCGTCTGCATCTTCATCGAAGGACTGCATTCTCCTTGCGGCCTGTGAGGCACATCAAACTCTCCCACAGAGCGCAGAAT
upper sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 5
gtatgctaca-tgc---ttctaattaacatatgtttctctgtgctcgaagatgaaggtcatcatgatttatgggcttgtttttgtttttgttcctggattgtctaatattcataacgact--tttgtttactt-cagCGCCTAGATTGGAGT---TCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
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gtattcaacagtgccttttctgttaaatgcttaatttttta-atgtggtgattttggttgtaatgatgc-tagaattga---tatcattattctctgattctctggattttaataagattggttgatcttctggcagCTCCACGATTGGAATGCTTCTGTTTCCTCTGGATCTGCA---AGGGATTGCATTCTGCTTGCAGCCTGTGAAGCACATGAAACTCTTCCTCAGAGTGCTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtttttgttcctggattgtctaatattcataacgacttttgtttacttcagCGCCTAGATTGGAGTTCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
tcataac putative branch site (score: 2)
cttttgtttacttc putative PPT
tctaatattcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctacatgcttctaattaacatatgtttctctgtgctcgaagatgaaggtcatcatgatttatgggcttgtttttgtttttgttcctggattgtctaatattcataacgacttttgtttacttcagCGCCTAGATTGGAGTTCTAGCTCCTCTGCATCTTCACGGAAGGACTGCATTCTTCTTGCTGCCTGTGAGGCACATCAAACTCTTCCTCAGAGTGCAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC