Sequence
atgc intronic sequence ATGC exonic sequencegtatttctccactcaatatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18100.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
-------------------gtatttctcc----actca-atatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
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ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttccctt-attctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 10
-----------------------gtatttctccactcaatatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
| | | | | | | ||| | | | | || |||||||| | | ||| || ||||||| | || || |||||||||||||||||| ||| ||| |||||||| ||||||||||| || | ||||||
agatattatatgatttctgtgggggaatcatgcgtttatctgttaaataagatgttccctttcttattgattccgaggcactgcttctgtttattggcagCTGAACTGGTCGAGAGAGTTGTTCTTCTTGGATTACCCATTGCAATCAAGGATGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
gtatttctccactcaatatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
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gtaactggt-accctcaagctgtttgtgatggatggtttgtattgcattaatga-tgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
ctttaac putative branch site (score: 3)
catttttc CT-rich tract
tttaacacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttctccactcaatatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA