Sequence
atgc intronic sequence ATGC exonic sequence...tttggacctttttgttttgcacctttgtcgagttgttcttttcgtttttgcttcttttatatatactcaagtgtttttatgtgacttatgttgccgacagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 3
-----tttggacctttttgttttgcacctttgtcgagttgttcttttcgtttttgcttcttttatatatactcaagtgtttttatgtgacttatgttgccga-cagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
| || | || | ||| ||| | || | || ||| | || || || | | | |||| | | ||||||| | ||||||||||| |||| || || | |||||||||| ||||| || | |||| ||| ||||||||||||||||||||||||||||||| || ||
aaaggtctgaattttctaaaa--gcagtttt-ttgatgtattttttatatgcttactagttactactttgtgtagatgttaacactt---ccatgttgcaaaacagGTGATTGGTTCAGGAACTGACAAGAAAAGGATTCCTGGCATTGATATCCACTTGAACGATGGTGATAAGTGGATGTTTGCTGGCCATGAGGTGCGTGTAA
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 3
------tttggacctttttgttttgcacctttgtcgagttgttcttttcgtttttgcttcttttatatatactcaagtgtttttatgtgacttatgttgc-cgacagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
| || | |||| | ||| ||| || | || ||| | || || || | | | |||| | | ||||||| |||||||||||| |||| || || || |||||||||| ||||| || | |||| ||| | ||||||||||||||||||||||||||||| || ||
aaaaggtctgaa--ttttcgaaaagcagtttt--tgatatattttttatatgcttactagttactactttgtgtagatgttaacactt---ccatgttgcattacagGTGATTGGTTCAGGAACTGACAAGGAAAGGATTCCTGGCATTGATATCCACTTGAATGATGGAGATAAGTGGATGTTTGCTGGCCATGAGGTGCGTGTAA
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 5
--tttggacctttttgttttgcacctttgtcgagttgttcttttcgtttttgcttcttttatatatactcaagtgtttttatgtgacttatg--ttgccgacagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
| || | | || |||||| | | | | || |||| | ||| | |||| | | | ||||| || || || | |||| ||||| || | |||| || ||||| |||||||||||||| ||| || |||| ||| | || |||||||||||||| ||||||||||| ||
tttgtgaagcagttcattttgcccatgctt---atgattttttttgaaattg-taaacttatgcttttttgtgaagttttaccctttttgtgggtttcttgtagGTAATTGGTTCTGGAATAGACAAGGATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgcttcttttatatatactcaagtgtttttatgtgacttatgttgccgacagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
ttcttttatatatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttggacctttttgttttgcacctttgtcgagttgttcttttcgtttttgcttcttttatatatactcaagtgtttttatgtgacttatgttgccgacagGTGATTGGATCAGCTGTAGATAAAGATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actcaag