Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaattttattttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G43780.1 (Glycine max), 3'ss of exon 2
gtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaattttattttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCAT-ACTAGCTAGTGTTGATC
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---------------------atccttatttctatttg--aagctacatataatagttttattttgctatttaaactttatacaaatatatgtgt-tcatgtagaaagtggaacttttttg----cagGATGTTTATTGAGTCATGCAAGAGGTTGAGGATTATGAAGAGATCAGATGCAAAGGGCTTCGATCTGCAACCAAAAGGGTCTTTAAAAGGATTTATAGAA-
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G01560.1 (Glycine max), 3'ss of exon 2
gtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaattttattttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
|| | || | ||| || || | | | | | | | | || | | ||| | | || | ||| | || | | ||| | | | | ||||||||||| || |||||||||||| ||||||| |||||||||||||||||| || || | ||| || | | | || | || | | |
----------------------tttctatttgaagctat---atataatagttttattttgtt--attttttctattttaaatttatacaagtatatgtgttcatatagaaagtgggacttttg-cagGATGTTTATTGAGTCATGCAAGAGGTTGAGGATTATGAAGAGATCAGATGCAAAGGGCTTCGATCTGCAACCAAAAGGGTCTTTAAAGGGATTTATAGAA
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G03840.1 (Glycine max), 3'ss of exon 2
gtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaatttta--ttttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
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---------------------------atgatgattttatatttgtatccatat---cttttttaagctatagtgattttctattttgtgatgtaaaacttatgtgtttgagatcatgttaccctaacagAATGTTTATGGAGTCATGCAAGAGGCTGAGGATTATGAAGAGGTCAGATGCCAAGGGCTTCGGTTTGCAACCAAAAGGATCTCTGAAGGGATTCATAGAA
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G22190.1 (Glycine max), 3'ss of exon 2
gtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaattttattttttaaattgt--aaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
| | || || | |||| | | || | | ||| || || | | | ||||| || | | || | ||| | | || | ||| ||||||| || |||||||||||||||||||| |||||| ||||||||| | || || ||| | || | | | ||| | || | | |
--------------------------agtaaatgatgat-gattttatccatat---tttttctaagctattgtgattttctattttgtgatgtaaaacttatatgtgtttgatcatgttactttaacagAATGTTTATGGAGTCATGCAAGAGGCTGAGGATTATGAAGAAATCAGATGCGAAGGGCTTCGGTTTGCAACCAAAAGGATCTTTAAAGGGATTCATAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagtcaaaaatttgtaattttattttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
ttttttttgtc CT-rich tract
aaaaatttgtaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttatgtttagcttgcattacaatgctcaattatcaaatttaccaaaatgaatataattaacctcttacaagtcaaaaatttgtaattttattttttaaattgtaaattttttttgtcggcagGATGTTTAAAGAATCATGCAAGAGGCTGAGGATCGTGAAGAGATCAGATGCAACTGGTTTTGGTCTCCAGCAAGATTAATCATACTAGCTAGTGTTGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA