Sequence
atgc intronic sequence ATGC exonic sequencegtacttatctccaagactcttttatttagtaaagactgtttttggaagagaatgcaaaggtgaaactgtgttttactaaattatggtttgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 4
-----gtacttatctccaagactcttttatttagtaaagactgtttttggaagagaatgcaaaggtgaaactgtgttttactaaattatggtt-tgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
| |||| | | | |||| | || || ||| | | || | || || | | | |||||| | | |||||||||| |||||||||||||| |||||| ||||||||||||||| ||||||||| ||||| || |||||| |||||||||| || |||||||||||||
aaagtgagtttatatatgatggttcacaatttggaaa------ttcttgaaccaatatatttggatggaagaataatctctattgatatggtgattttccatttagGATGAGGCTGGAACAGCAGCCATTAAAAATGTTGAACTCGATGCATCTCTTGGAGGACGTGCAGTGCAACACAGGGAAATTCAAGGGCATGAATCTGACA
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 3
------gtacttatctccaagactcttttatttagtaaagactgtttttggaagagaatgcaaaggtgaaactgtgttttactaaattatggtttgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
| | || || | ||||| || | | || | | | | || || || | || | || || ||| | || |||||||| |||||||||||||| ||||||| |||||||||||||| ||||||||| ||||| || |||||| |||||||||| || |||||||| ||||
ttttctctttctggttctaaagttggtttatgtatgatggttcaaagtttggaaattcttgaaccaataatctctattg----atatggtgattt--tccttgtagGATGAGGCTGGAACAGCAGCCATTAAAACTGTTGAACTCGATGCGTCTCTTGGAGGACGTGCAGTGCAACACAGGGAAATTCAAGGGCATGAATCCGACA
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 3
gtacttat-ctccaagactcttttatttagtaaagactgtttttggaagagaatgcaaaggtgaaactgtgttttactaaattatggtttgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
||| | | || | | ||||| || | | | ||| | | ||| || | | | || || | || || |||| | || || |||||||| |||||||||||||| | ||||| ||||| || ||| | ||||||||||| ||||| || |||||| | ||| |||| || | || |||||||
gtattactacttccttttgttcttattcag---aaattacacttgtagtaaaat--aacgtttatgcttgaaattgc-aacttctggtcttatcat---agGATGAATCTGGAACAGCAGCTATAAAAACTGTTGAGCTTGATACTGTTCTTGGAGGGCGTGCAGTACAACACAGAGAACTTCAAGGCTACGAGTCTGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagaatgcaaaggtgaaactgtgttttactaaattatggtttgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
tgttttactaaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttatctccaagactcttttatttagtaaagactgtttttggaagagaatgcaaaggtgaaactgtgttttactaaattatggtttgatgattttagGATGAAGCTGGAACAGCAGCTGTTAAAACAGTTGAACTCGATGCAGTTCTTGGAGGCCGTGCTGTCCAACACCGGGAAATTCAGGGTCATGAATCTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG