Sequence
atgc intronic sequence ATGC exonic sequencegtcagttgtttctgaatgcaactccatgctgtctttttgtaatgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
-------------------gtcagttgtt-tctgaatgcaactccatgctgtctttttgtaatgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
| ||||||| | || | ||| || | | ||| | || | ||| ||| | | | || || | | || |||||||||||||| |||| || ||||| ||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattacta--gatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
upper sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
-------------------gtcagttgtt-tctgaatgcaactccatgctgtctttttgtaatgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
| ||||||| | || | ||| || | | ||| | || | ||| ||| | | | || || | | || |||||||||||||| |||| || ||||| ||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattacta--gatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG
upper sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
gtcagttgtttctgaatgcaactccatgctgtctttttgta-atgcagctgtggttatatgttat-------tttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
|| |||| | | || || |||||||| || | | | |||| | || || ||| | | | || |||| ||||||||||||| |||| || ||||| ||||||||||||||||||||||||
---gtatgcttctaaccatca-tctata-tgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
upper sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
gtcagttgtttctgaatgcaactccatgctgtctttttgta-atgcagctgtggttatatgttatt-------ttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
|| |||| | | || || |||||||| || | | | |||| | ||| | ||| | | | || |||| ||||||||||||| |||| || ||||| ||||||||||||||||||||||||
---gtatgcttctaaccatca-tctata-tgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
ttatatgttattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttgtttctgaatgcaactccatgctgtctttttgtaatgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG