Sequence
atgc intronic sequence ATGC exonic sequence...actgcactgtatattatgctgcaataaattcaatttattggttagaaatgtggtctattatatttaatccatttgcaacatattttatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10350.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
--actgcactgtatattatgctgcaataaattcaatttattggttagaaatgtggtctattatatttaatccatttgcaacatattt-tatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
|| | | || || || | | | | | | | || || | ||||| || || ||| || | ||| | | | | ||||||||||||| |||||||| || |||||||| | |||||| |||||||||||| | |||||||||||| | || | ||| || | ||| ||||
cttttggatttgatttt-tgttttcaaagctactaggggt-ggataatcacgtggtgtaaactacgtaaat-gcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 2
actgcactgtatattatgctgcaataaattcaatttattggt-tagaa--atgtggt-ctattatatttaatccatttgcaacatattt-tatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
| | || || | | | || | | | | | ||||| | ||||| | | | | | || | ||| | | | | ||||||||||||| |||||||| || |||||||| | |||||| ||||| |||||| | | |||||||||| | || | ||| || ||||| ||||
-----gatttgatttttgttttgaaagatactaggggtggatatagaatcacgtggtgtcaattaactacaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtggtctattatatttaatccatttgcaacatattttatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
atttaat putative branch site (score: 4)
tattatatttaatcca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgcactgtatattatgctgcaataaattcaatttattggttagaaatgtggtctattatatttaatccatttgcaacatattttatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - -caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacata