Sequence
atgc intronic sequence ATGC exonic sequencegtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60640.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G07260.1 (Glycine max), 3'ss of exon 8
gtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
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gtaa-gttattttgttgtacatccatgttctgttggccagatttttcgtgtctgacatttgctaact-tgatgacagAATGACGGTGATGTGAAAATAGTTGTTGGGAATAACTTTGATGAAATTGTTTTGGATGAGTCAAAGGATGTTTTGCTTGAG
upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G20630.1 (Glycine max), 3'ss of exon 8
gtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggt-ggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
|||| | |||| |||| | | | | | | | | || | | | || | | |||||| |||| |||||||||||||| ||||| ||||||||||||||||||| |||| || || || ||||| || || |||
gtaa-gttattttgttatcagtccgtgttccattggccaaaattttcatgtctgacatgttttcttacttgatgacagAATGATGGTGATGTGAAAATAGTTGTTGGTAATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG
upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 8
-------gtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
| | | | | |||| | | || | | | | || | ||| |||||| |||| |||||||||||||| ||||| |||| |||||||||||||| |||| || || || ||||| || ||||||
gtatgttatttaattttcccaccgtcaattatgtcctattaatttagtttttcatgcctaacgtgtttgctaacttggtaacagAATGATGGTGATGTGAAAATAGTAGTTGGTAATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG
upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G29550.1 (Glycine max), 3'ss of exon 8
-------gtaaagccgttttattatta--atttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
| || | || | || | | | || | |||||| || | ||||| |||||| |||| |||||||||||||| ||||| |||| |||||||||||||| |||| || || || ||||| || ||||||
gtatgttacttaatttttccaccataattatgttctattaatttagtttttcatgtctaacgtgtttgctaacttggta---acagAATGATGGTGATGTGAAAATAGTAGTTGGGAATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG
upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g02890.t01 (Vitis vinifera), 3'ss of exon 8
---------gtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
||| ||| || | ||| | | | | | || || | | | || |||||| | | |||||| ||||| ||||||||||||||||| || |||||||| |||||||||||| |||| || || || ||||| ||||| |||
gtgagttacctaattttgttgtactgttattaaattgtcatttcatgttctaatccattatcctt-ctatattttgattgacacagAATGATGAGGATGTGAAAATAGTGGTCGGGGATAACTTCGATGAAATTGTTTTGGATGAATCAAAGGATGTTCTTCTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
aaacttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagccgttttattattaatttccaaccgtcttgttggctcatgtaacaccgaaacttaattttggtggctacagAACGATGAAGATGTGAAAATAGTGGTTGGAGATAACTTTGATGAAATTGTTCTGGACGATTCTAAAGATGTGCTTCTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG