Sequence
atgc intronic sequence ATGC exonic sequence...aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttcattgatatgcttttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G33230.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 5
aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttca-ttgatatgcttttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
|| | | || | | || | | | | || || | || | || | | | | | | || ||| || ||||||| | ||||||||||||| ||| |||| ||| |||| || |||||||||||||| || ||||| |||||| |||| | | ||||||
-gggcggacaggaattttatttggtttgcgtgttgatattgtcatccttacattgcatattgggaaaccttttggcaaataaacttactatatggttacagGTGGATATATCATCATTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
upper sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 4
aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttcattgatatgctt---------ttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
| || |||| || | | ||||| | ||||| || | | || ||| || || ||| ||| || ||||||| | |||||||| |||| ||| |||| ||| |||| || |||||||||||||| || ||||| |||||| |||| | | ||||||
-------gggaggacagaaattttattcggtttgcgtgttaatattgtcatccttacattgcatattgg--gaaatcttttggcaaataaacttattatatggttacagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
upper sequence: AT1G33230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 3'ss of exon 5
---aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttcattgatatgcttttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
| | | | | | || ||| | | | ||| | | | ||| ||| || || | | || ||||||||| |||||||| | || ||||| |||| ||| ||| |||| | || || |||||||| ||||||||||| || ||||||||||||| || ||||||
aactgacaacaatatgatactg-tttaaactttcatatatttggttagttttattagtatcatctgtcatagcttacaaaaaatccc--atatgctttcgcagGTGGATATACCATCACTATTGTGCTATGATTATGGCTCTCGTTAGTCTCACATGGGAAATCAAGGGACAACCAAACTGCGCACAAAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatcctctcaatcgaagatgactaaaacctcttcattgatatgcttttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
tgctttt CT-rich tract
attgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggccttagtgggttgatgatttggatctgaagttatcttaatgtatatatcctctcaatcgaagatgactaaaacctcttcattgatatgcttttgcagGTGGCTTTATCATCATTATTTTGCAATGGCTATGTCCCTTGTCAGTCTCACTTGGGAAATCAAAGGTCAACCAAACTGCGTTCAGAAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - gatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - ctctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaa