Sequence
atgc intronic sequence ATGC exonic sequence...tcaccccttatacttttgtgaactgcagctagcatgtttgcaaaatttgatgatcttttcttgagttttgtctatcatgacaatggatgcttatctttagGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 6
-tcaccccttatacttttgtgaactgcagctagcatgtttgcaaaatttgatgatcttttcttgagttttgtctatcatgacaatggatgcttatcttt-----agGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
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gttagtttgtggaccttttcagctttctg-----atgcttgaagtactttagcttatatttatgttgattaacttaaatttttttgtttgttttcccttctgaaagGTTGGATACAAAGTTCGTCTGGAGGGTATGAAAGGGAGAGATACTCGTCTTCTTTTTTGCACCACGGGTGTATTATTGCGGAGACTGCTTGTGGATAGGA
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 6
-tcaccccttatacttttgtgaactgcagctagcatgtttgcaaaatttgatgatcttttcttgagttttgtctatcatgacaatggatgcttatcttt-----agGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
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gttagtctgtggaccttttccacttgctg-----atgcttgacgtactttagcttatatttatgttcattaacttaaattattttgcttgttttcccttctgaaagGTTGGATACAAAGTTCGCCTGGAGGGTATGAAAGGGAGAGATACTCGTCTTCTTTTTTGCACCACAGGTGTATTATTGCGGAGATTGCTTGTGGATAGGA
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------tcaccccttatacttttgtgaactgcagctagcatgtttgcaaaatt-tgat-------gatcttttcttgagttttgtctatcatgacaatggatgcttatcttt----------agGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
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gtaagttttacgctctgtgaccagtttttgtgaatttttttgacactggaatatttaatctacctatattgatttattggaatg-aacaaatctgatttcaacactatgacataagtggaagttctataatgtgacaaaacttatggaggttgattcgcactctcttctcttggaagGTTGGCTACAAAGTGCGGCTTGAAGGAATGAGAGGGAGAGATACACGTCTTCTTTTTTGTACAACTGGTGTTTTACTTAGAAGGTTACTTGTGGATCGTA
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------tcaccccttatacttttgtga-actgcagctagcatgtttgcaaaatttgat-gatcttttcttgagttttgtctatcatgacaatggatgcttatctttagGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
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gtaagtttctgattgcattttaggaatcttgcttctgatcattttgatctgtctaagactaatgtaaaaatacctataaaaaaaaaaagaagattaatataaaaatatct-ccatttca--tgat-cttttctaaagGTTGGTTATAAAGTTCGGCTGGAGGGAATGAAAGGGAGGGACACTCGCCTTCTTTTTTGCACTACTGGCATATTATTGAGAAGATTACTTGTTGACAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatgatcttttcttgagttttgtctatcatgacaatggatgcttatctttagGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
atttgat putative branch site (score: 5)
cttatcttt putative PPT
ttatcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaccccttatacttttgtgaactgcagctagcatgtttgcaaaatttgatgatcttttcttgagttttgtctatcatgacaatggatgcttatctttagGTTGGCTACAAAGTTCGGCTGGAAGGCATGAGAGGAAGAGATACGCGCCTTCTTTTCTGCACCACTGGAGTCCTGTTGCGGAGATTGTTGGTGGACAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - ctgcagc
- - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - -tttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgc