Sequence
atgc intronic sequence ATGC exonic sequencegtttgaattttaaaccatttgttacttttttttttgcgttcaccgtgcatatccttgcttgttaatctgactgttcaaacttgaattgaaatttcctttaccttcgctgctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18520.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G13000.1 (Glycine max), 3'ss of exon 6
gtttgaattttaaaccatttgttacttttttttttgcgttcaccgtg-catatccttgcttgttaatctgactgttcaaacttgaattgaaatttcctttaccttcgctgctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
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----------------------------------------aactataatgtatcttta---gtacctctggtacttttatct--aataaaaact------actttcgctg-tccaaaaaaaaaaattatgattaatgtctctgtgatt-------------gcagTTATTTCACTTCTGACACATATGCCAATGAGCATTCAGCACTTGCTGCTAGGTTGGCAGCTGGGTTATGTGCTGATCTAGCATCAGCAATTGTTTCTGAG
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G07990.1 (Glycine max), 3'ss of exon 9
gtttgaattttaaaccatttgttacttttttttttgcgttcaccgtgcatatccttgcttgttaatctgactgttcaa-acttgaattgaaatttcctttaccttcgctgctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
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-----------------------------------------------------------tattcaatt--ccattcaatgctttagtgttaggatgcttaatgctttttgctttatgttga---caggatgtattcattatgattaatgtctctgtgattg-cagTTATTTCACGTCTGATACATATGCCAATGAGCATTCAGCACTTGCTGCTAGGTTGGCAGCTGGGTTATGTGCTGATCTAGCATCAGCAATTGTTTCTGGG
upper sequence: AT3G18520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv17s0000g04120.t01 (Vitis vinifera), 3'ss of exon 10
gtttgaattttaaaccatttgttacttttttttttgcgttcaccgtgcatatccttgcttgttaatctgactgttcaaacttgaattgaaatttcctttaccttcgctgctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
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------------------------------------------------------------aattatgcggtaccatgagattgggt--atatcagctgttgcattagtgttgtttctgagatgagctaggttttctaaatggttagtt--ccattgactggcagTTATTTCACTCCTGATACATATGCTAATGAGCATTCAGCACTTGCTGCTCGGCTTGCAGCTGGTTTATGTGCTGATCTTGCTTCTGCAATTTTTTCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
tcttgat putative branch site (score: 4)
atttatctcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgaattttaaaccatttgttacttttttttttgcgttcaccgtgcatatccttgcttgttaatctgactgttcaaacttgaattgaaatttcctttaccttcgctgctcctcatttatctctttttgctcttgatcccgttcttttaccattgtctggcagCTACTTCACCTCTGACACATATGCTAATGAGTATTCAGCACGTGCTGCTAGACTTGCAGCAGGTTTGTGCGCTGATCTAGCTACAGATATTTTCACTGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT