Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatgccacaagtttggatgccctcctatcatgtgtttagatttcaaaaaataccctatttcttcatggctacagttttttttttttttaattctgcttatatgttcatttctgctttggaatctcaaatcaattattacattgatgacatgttcgatgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34830.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G03760.1 (Glycine max), 3'ss of exon 7
gtaagcatgccacaagtttggatgccctcctatcatgtgtttagatttcaaaaaataccctatttcttcatggctacagttttttttttttttaattctgcttatatgttcatttctgctttggaatctcaaatcaattattacattgatgacatgttcgatgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
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------------------------------------------------gtacaattattgcaacttgt-atttctaaagaactatattcacagtggtatgagt-tgagttcctcccagtttt----ttttaattgtac----atgctgatgtgatgtttaatgcagtagAATGTGAAGCCAGACCGTGTTGTATTCAATGCACTTATAGCTGCCTGTGCTCAATCAGGAGCAGTAGATCGTGCTTTTGATGTGTTAGCAGAAATGGCAG
upper sequence: AT4G34830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G35270.1 (Glycine max), 3'ss of exon 6
gtaagcatgccacaagtttggatgccctcctatcatgtgtttagatttcaaaaaataccctatttcttcatggctacagttttttttttttttaattctgcttatatgttcatttctgctttggaatctcaaatcaattattacattgatgacatgttcgatgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
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--------------------------------------gtacaattattgcaaaatg---tatttctaaagaactata-ttcacagtggtatgagtt--------gagttcctcccagttttttaattgtacat----------gctgatgtgatgtttaatgcagtagAATGTGAAGCCAGATCGTGTTGTATTCAATGCACTTATAGCTGCTTGTGCCCAATCAGGAGCATTAGATCGTGCTTTTGATGTGTTAGCAGAAATGACAG
upper sequence: AT4G34830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv03s0038g01320.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcatgccacaagtt-tggatgccctcctatcatgtgtttagatttcaaaaaata--ccctatttcttcatggctacagttttttttttttttaattct--gcttat--atgttcatttctgc-tttggaatctcaaatcaattattacattgatgacatgttcg-atgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
| ||| ||| | ||| || | || | |||| | || | || || |||||| ||| || ||| | | || |||| | || || |||||| ||| |||| | |||| | || | | | |||| | ||||| ||||||||||| || ||||||| || |||||||||||||| || ||| ||||||||||||||||||||||||| || |||||||||||||||||||| ||||||| ||
----gtatgattttagtcatagattttctaatctcctttgttagcacttttctttttcgttccaatgatttcatgtctatggtagtttgtacaagaacatcccagcttgttcatttttgcttctgcattttgaatattaaataagtt-tcaaactgataagatgttgatatgcagtagAAAGTGGAGCCAGATCGAGTTGTATTCAATGCACTTATCACTGCATGTGGTCAATCAGGAGCTGTGGATCGTGCTTTTGATGTGTTAGCAGAAATGAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgctttggaatctcaaatcaattattacattgatgacatgttcgatgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
cattgat putative branch site (score: 4)
aaatcaattattacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatgccacaagtttggatgccctcctatcatgtgtttagatttcaaaaaataccctatttcttcatggctacagttttttttttttttaattctgcttatatgttcatttctgctttggaatctcaaatcaattattacattgatgacatgttcgatgcagtagAATGTTAAGCCAGACCGGGTTGTATTCAATGCCCTCATCTCTGCATGTGGTCAATCAGGAGCTGTCGACCGTGCTTTTGATGTGTTAGCTGAAATGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA