Sequence
atgc intronic sequence ATGC exonic sequencegtatcattttcgtcccctgcatttctctgcacttttatctatcgctttccaccaatatttacctttcttacgtggtctatgacattgtcttcagCCTGCTTTAGGTGCTGACGGCAAGAAAGTTGAATCTCAGAGCAACGTCCTTCTCGGTTTGATTGAGAATATGCAGTATGCTGTCACTGTGGATGTTCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC190743.3_FGT012 (Zea mays), 3'ss of exon 1
--------gtatcattttcgt--cccctgcatttctctgcacttttatctatcgctttccaccaatatttac-ctttcttacgtggtctatgacattgtc-ttcagCCTGCTTTAGGTGCTGACGGCAAGAAAGTTGAATCTCAGAGCAACGTCCTTCTCGGTTTGATTGAGAATATGCAGTATGCTGTCACTGTGGATGTTCTTC
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gtatttatttactttttcagaagatcatgggcattctagtatttcaattgtctgtttttctcttttatgtaaacttgctgttttgccttttgatgttctggcacagCCTGCTGTTGGAGCTGACGGAAGGCAAGTGGAGGCTCAAGGCAATGTTCTTCTTGCATCAATTGAGAATATGCAATATGCTGTTACTGTAGATGTTCTTC
upper sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 6
gtatcattttcgtcccctgcatttctctgcacttttatctatcgctttccaccaatatttacctttcttacgtggtc-tatgacattgtcttcagCCTGCTTTAGGTGCTGACGGCAAGAAAGTTGAATCTCAGAGCAACGTCCTTCTCGGTTTGATTGAGAATATGCAGTATGCTGTCACTGTGGATGTTCTTC
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----------------------------gtaaattt-tttacagttgaatatttattgaaatttttaccatgtactaacaggttgttctatccagCCTGCTTTAGGTCCTGATGGCAAGAAAAAAGAACCTGAGAGTAATGTTCTTCTTGCTTCAATTGAGAATATGCAATATGCTGTTACAGTAGATGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcgctttccaccaatatttacctttcttacgtggtctatgacattgtcttcagCCTGCTTTAGGTGCTGACGGCAAGAAAGTTGAATCTCAGAGCAACGTCCTTCTCGGTTTGATTGAGAATATGCAGTATGCTGTCACTGTGGATGTTCTTC
ttcttac putative branch site (score: 2)
ttgtcttc putative PPT
aatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcattttcgtcccctgcatttctctgcacttttatctatcgctttccaccaatatttacctttcttacgtggtctatgacattgtcttcagCCTGCTTTAGGTGCTGACGGCAAGAAAGTTGAATCTCAGAGCAACGTCCTTCTCGGTTTGATTGAGAATATGCAGTATGCTGTCACTGTGGATGTTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG