Sequence
atgc intronic sequence ATGC exonic sequencegtaagactagtttctctgcaaattcagcacgcagccttacatgaaggacattaaactcttatatcactctttaggctttatgttgtaaactatacttgttgattggcagattttggaatatcatgagtcttttagcttgttgtaaccgtgtatgtttaaatcgacagGAGCTATTGGCGATACAGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43945.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0042g00120.t01 (Vitis vinifera), 3'ss of exon 1
gtaagactagtttctctgcaaattcagcacgcagccttacatgaaggacattaaactcttatatcactcttta-ggctttatgttgtaaactatacttgttgattggcagattttggaatatcatgagtcttttagcttgttgtaaccgtgtatgtttaaatcg-acagGAGCTATTGGCGATACAGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCT
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------------------------------------------------------------ccataattccatatgattctctgttgcaa------catggaagcaccctgctttcccctttctgctaatttctt---tgggtatgcctatatttattttatttttgcagGAGTTATTGGCCATTCAACAAGAAGGGCCAAGAGCTATTGGCTTCTTTGGGACACGAAATATGGGATTCCTGCATCAAGAACTTATCGAGATCCTGAGCT
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 3
gtaagactagtttctctgcaaattcagcacgcagccttacatgaaggacattaaactcttatatcactctttaggctttatgttgtaaactatacttgttgattggcagattttggaatatcatgagtcttttagcttgttgtaaccgtgtatgtttaaatcgacagGAGCTATTGGCGATACAGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCT
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-----------------------------------------------------------agttgcaatgagcaagcattctaggttttcccctttctattgatt------tttatgaacatctt--attgtggattttaaagttgctatgtgcgaattattttgcagGAGTTATTGGCCATCCAACAACAAGGGCCAAGAGCTATTGGGTTCTTTGGGACAAGGAATATGGGATTCACACATCAAGAACTTATTGAGATTCTCAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaatatcatgagtcttttagcttgttgtaaccgtgtatgtttaaatcgacagGAGCTATTGGCGATACAGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCT
ttgtaac putative branch site (score: 2)
tatgtttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactagtttctctgcaaattcagcacgcagccttacatgaaggacattaaactcttatatcactctttaggctttatgttgtaaactatacttgttgattggcagattttggaatatcatgagtcttttagcttgttgtaaccgtgtatgtttaaatcgacagGAGCTATTGGCGATACAGCAGCAAGGTCCTAGATCAATTGGCTTCTTTGGGACAAGAAATATGGGTTTCATGCATCAAGAACTGATTGAGATACTTAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC