Sequence
atgc intronic sequence ATGC exonic sequencegtctgtcctttttcatctcgatgcggatttacgttttccttcgtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39390.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39390.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G15250.1 (Glycine max), 3'ss of exon 2
-----------gtctgtcctttttcatctcga-----tgcggatttacgttttccttcgtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
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gtaacaactatattttttttttttatctttgaaagtatcaagttttaacactgccagtgacaaagataggtatttatactgtttccttcctttgaaatgaaaacttcagATTGCTAAGCTGAGTATGATTCCAGTATCTTGTTTCCTGGAAGTTATCTTGGACAATGTGCGATATTCAAGGGACACAAAACTTAGCATTTCTCTAGTTC
upper sequence: AT4G39390.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G31940.1 (Glycine max), 3'ss of exon 4
---------gtctgtcc---tttttcatctcgatgcggatttacgttttccttcgtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
| | | | ||||| || |||| | || | || || | || || | | | | | |||||||| |||||||||||||| || || |||||| | || |||||||| | || ||||| | |||||||| || ||||| |||||||||| ||||||
gtaactagattttttacaaattttttgaaagtatcaaattttaacactgccagtgacaaaggtaggtatttatagtgtttccttctcttgaaatgaaaacttcagATTGCTAAGCTGAGTATGATTCCAGTATCTTGTTTCCTGGAAGTTATCTTGGATAATGTGCGATATTCAAGGGACACAAAACTTAGCATTTCTCTAGTTC
upper sequence: AT4G39390.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 3
gtctgtcctttttcatctcgatgcggatttacgttttccttcgtttaaagttttttttagtaagatcttgaaacgagtgtgtt-------ggcattg----cagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
||| |||| | | ||| ||| ||||| | | |||||| || | | || || | ||| |||||||||||||||||||||||||| || || ||| |||| |||||| || | ||||| | |||| ||||| || || ||||||||||| | |||||||
----gtcagttttgggaactgc-tgactttttgttctccttttgctctcatattttttttcaaagttacaagttatgttctttctcttcaaactttgatgtcagATTGCGAAGCTGAGTATGATCCCAGTCTCATGTGTTCTCGAAGTTGTGTTGGACAAGATGCGGTACTCAAGGGACACCAAGCTTAGCATATCATTAGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcgtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
tttaaagtttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtcctttttcatctcgatgcggatttacgttttccttcgtttaaagttttttttagtaagatcttgaaacgagtgtgttggcattgcagATTGCGAAGCTGAGTATGATCCCGGTTTCTTGTCTTCTAGAAGTTATGCTTGACAATGTCAGGTATTCAAGAGATACAAAGCTTAGCATTTTGTTAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA