Sequence
atgc intronic sequence ATGC exonic sequence...tatagactgcccactcatgctaaatttctcaataagtcgttattgtgttccttaaaccctatatgcatcagtggattaagtttaccttttctccttttagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39630.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G10150.1 (Glycine max), 3'ss of exon 5
---tatagactgcccactca-tgctaaatttctcaataagtc-gttattgtgttccttaaaccctatatgcatcagtggattaagtttaccttttctccttttagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG
| | | | ||| | | |||| | ||| || | | | || | | || | || | | || || || | || |||| || ||| ||||||||||||||| ||||| |||||||||||||||||||| || | || || |||||| | ||||| ||||||| || | || |
ctctttgctcaacttactttcttccaaatgcatttgtaactctgcggatacacttct-acattctcttcacaatggacgcttgagcagg----ttgtaattgcagGTTGTAATTATTGATGATGGAAGTGCTGATGAGACAAAAAGAGTAGCTTTTGAATTTGTGAGGAAATACACAGTAGACAAGGTAAGGGTCATCCTTCTAG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G52810.1 (Glycine max), 3'ss of exon 5
tatagactgcccactcatgctaaatttctcaataagtcgttattgtgttccttaaaccctat--atgcatcagtggattaagtttaccttttctccttt--tagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG-
||| | || |||| || || | | || | || || | | || | || || | ||| || || | ||| |||| || ||| ||||||||||||||| ||||| |||||||||||||||||||| || | || || |||||| | ||||| ||||||| || | || |
-atatttgaatctctt-tgctcaactt---actttgttccaaatgcatttgtaactttctgtggatacacttctacattctcttcacaatggacacttgagcaggTTGTAATTATTGATGATGGAAGTGCTGATGAGACAAAAAGAGTAGCTTTTGAATTTGTGAGGAAATACACAGTAGACAAGGTAAGGGTCATCCTTCTAGG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g01230.t01 (Vitis vinifera), 3'ss of exon 5
------tatagactgcccactcatgctaaatttctcaataag--tcgttattgtgttccttaaaccctatatgcatcagtggattaagtttaccttttctccttttagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG
|| ||| ||| | |||| | || | | | | | ||| || | | || | ||| | || | | | | | ||||||||||||| ||||||||||||| |||||| ||||| |||||||||||||| || | | ||| |||||||| ||||| | |||||||||| ||||
ttacaggatgtcctgattactatctccaaatagcaacatgggctttatcctagcattctctacttctctcacatat-actggggcatgtgttcttgtac-------agGTGGTGATTGTCGATGATGGAAGTGCTGATGGGACAAACAGAGTAGCTTTTGACTTTGTAAAAAAATACACAATAGACAATGTTAGGGTTATACTTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttccttaaaccctatatgcatcagtggattaagtttaccttttctccttttagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG
tttaccttttctcctt CT-rich tract
attaagttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatagactgcccactcatgctaaatttctcaataagtcgttattgtgttccttaaaccctatatgcatcagtggattaagtttaccttttctccttttagGTGGTGATTGTTGATGATGGAAGTGTTGATGGAACAAAAAGAGTAGCTTTTGATTTCATTAGAAAGTACACAATTGACAACATAAGGGTTATACCCCTTG
- - - - - ccactca
- - - - - - - - - - - - - - -caataag
- - - - - - - - - - - - - - - - - - - - - - - - - -ttaaacc