Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaatatagtccttttttactgtaaaaattagatatatatgttcaaccgttgtaacttttgatgtgaaacagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43600.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtatgtaatatagtcctttttta---ctgtaaaaattagatatatatgttcaaccgttgtaac-------ttttga--tgtgaaa--cagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
||| ||| | | |||| || || | || || | |||| || | | || ||| ||| | | ||||| ||||| || || || || ||||| |||||||||||||| || |||||||| |||||||||||||||||||| || || ||||||| |||
gtacttctcatttacttgttatacaatttttttctattcctattaatgtttttctttcttgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAGTTCCCGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
upper sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtatgtaatatagtccttttt----tactgtaaaaattagatatatatgttcaaccgttgtaac-------ttttga--tgtgaaa--cagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
||| ||| | | ||||| | || | || || | |||| || | | || ||| ||| | | ||||| ||||| || || || || ||||| |||||||||||||| || |||||| | |||||||||||||||||||| || || ||||||| ||||
gtacttctcatttacttgttatacaattttttttctattcctattaatgtttttctttcctgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCGGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAGT
upper sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtatgtaatatagtccttttttactgtaaaaattagatatatat-----gttcaaccgttgtaacttttga---tgtgaaa--cagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
|||| ||| | | | | |||| || || | | | | ||| | | ||||| | ||| | | ||||| | ||| || || ||||| |||||| |||||||| ||||| || |||||||| ||||||||| ||||||||||| || || ||| ||| |||
gtacttctcatttacttgttatgcaatttttttcctatttatattatttttttcctttctctttttggttttatgataaatactttctaaattgtcacatccagATCAAACTTGGGTCACAATATTACTTCTATATGGAGACCCAAACTGCCCTTGCAGTTCCAGATGAAGATAACTGCATTGTGGTTTACAGTGCAATACAAT
upper sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gtatgtaata-tagtccttttttactgtaaaaattagatatatatgttcaaccgttg-taacttttgatgtgaaacagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
|| || | || | | |||| || | | || | | | | || | || ||| | | || | | ||||| | ||| || || || ||| ||||| |||||||||||||| || |||||| | ||||||||||||||||||||| || || ||||||| |||
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggt-tttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgtaaaaattagatatatatgttcaaccgttgtaacttttgatgtgaaacagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
taaaaattagatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaatatagtccttttttactgtaaaaattagatatatatgttcaaccgttgtaacttttgatgtgaaacagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA