Sequence
atgc intronic sequence ATGC exonic sequencegtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcagTTATACTTGACAGACTTGGCAACAAGGGAGAGTGTTTTGCTGTGCACTAAGGAACATCCAATTCAACAATTAGCGTTGCAAGATAATAGTATATGGGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05090.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 8
----------------------------gtgagta-gacaccaaacttgttt---ctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcagTTATACTTGACAGACTTGGCAACAAGGGAGAGTGTTTTGCTGTGCACTAAGGAACATCCAATTCAACAATTAGCGTTGCAAGATAATAGTATATGGGTTG
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gtgagtgcagtttttcgataaatttttaattatcatgactttgaatttatatgatgtctccttgttttgcttaattagtgaagcttgtgttactgattcg---taattcttttatttttgt-agTTATACTTGACAGACTTGCAAACAAGAGAGAGTGTTTTGCTTTCAACCGGGGAAAATCCTATTCTTCAATTGGCTTTGCATGACGATAGCATTTGGGTTG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------------------------------------gtgagtagacaccaaacttgtttctttctttggttttct-----tccagcgtataacctccttttttaat-ttcatttat-------ctgttatgttt---ccgtcagTTATACTTGACAGACTTGGCAACAAGGGAGAGTGTTTTGCTGTGCACTAAGGAACATCCAATTCAACAATTAGCGTTGCAAGATAATAGTATATGGGTTG
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gtgagtacagttttctcccagaactcaaccaatgcaaatattcccctgcctctttcttatgttttgccattatttttttcctttagcatatgatgttttctcccttttttctttctctatctctctctctctctcttttctgatctttttctgcaatactcatcctttgatgcccaattctgtttatactctcagTTATACTTGACAGACTTGGCGACAAGAGAGAGTATTTTGCTTTGCACAAAGGAACATCCTATTTTGCAACTGGCATTGCATGATGATGGCATATGGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcagTTATACTTGACAGACTTGGCAACAAGGGAGAGTGTTTTGCTGTGCACTAAGGAACATCCAATTCAACAATTAGCGTTGCAAGATAATAGTATATGGGTTG
ttttaat putative branch site (score: 3)
tttccgtc putative PPT
ttttttaatttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcagTTATACTTGACAGACTTGGCAACAAGGGAGAGTGTTTTGCTGTGCACTAAGGAACATCCAATTCAACAATTAGCGTTGCAAGATAATAGTATATGGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA