Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcaccattgccagtcttgcacattaaagccacttatttgcttaaaatattgtctttcgtagtttcgtataaaaattattgtcttcatgtctttcatcgatgcagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 2
-----------------------------------------gtaagttcaccattgccagtcttgcacattaaa-gccacttattt-gcttaaaatattgtc--tttcgtagt--------ttcgtataaaa---attattgtcttcatg---tctttcatcgat------gcagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
|| | || | | ||| | | |||| | || || || | || ||| ||| |||| | | || || | | |||||| | ||| | ||| | | |||| |||||| |||| |||||| |||||||||| ||||||||||| || || | | || | | |||||||| || || | | ||||||||| |
gtaagtttggaagatgattgtttgtgtacttagaagatgcaatattgttctgatggtgttttttgtaaaataaataatagGTACTTAGCGTGGCATGCTGTGTATTTTATAGTCATTGTGGTACTTAGAAGATGCAATATTGTTCTGATGGTGTTTTTTGTAAAATAAATAATAGGTACTTAGCGTGGCATGCTGTGTATTTTATAGTCATTGTGGTAACCGTGCCATGTTAAGAGAGAGACCACTTGACCGAAGAAATTCTAACTGGTTTTCTT
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 2
gtaagttcaccattgccagtcttgcacattaaagccacttatttgcttaaaatattgtctttcgtagtttcgtataaaaattattgtcttcatgtctttcatcgatg-cagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
| ||| | | | || | | || | | |||| || || | | ||| | || || || | || | | || || || |||| |||||| |||| |||||| |||||||||| ||||||||||| || || | | || | | |||||||| || || | | ||||||||| |
--------------gtaagtttggaagatgatggt---ttgtgtccttagaagatg---caacattgttctg-atggtgttttttttttt--ttttttaaataaataatagGTACTTAGCGTGGCATGCTGTGTATTTTATAGTCATTGTGGTAACCGTGCCATGTTAAGAGAGAGACCACTTGACCGAAGAAATTCTAACTGGTTTTCTT
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttc--accat-tgccagtcttgcacattaaagccacttatttgcttaaaatattgtctttcgtagtttcgtataaaaattattgtcttcatgtcttt--catcgatgcagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
|||||| | | | ||| || ||| || | | ||| | | | || || | | | | || | | |||| | ||| | || || || ||||||| || || || |||||| |||||||||| |||||||||||||| ||| || |||| |||| |||| ||| ||| | || | | |||||||| |
gtaagtcctgatgacatgctggttgcttacactagatgttttctttttatcacagcctttggctttgca-tgtaaaattcagagccttgttctgatggccttattctctgtgtagGTTCTAAGTATAGCCTGCTGTGTATTTTATAGTCATTGTGGTAATCGTGCTATTTTGAGACAAAGACCATTTGAGAGAAGGAATTCTGGTTGGTTTTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctttcgtagtttcgtataaaaattattgtcttcatgtctttcatcgatgcagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
tctttcatc CT-rich tract
tagtttcgtataaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcaccattgccagtcttgcacattaaagccacttatttgcttaaaatattgtctttcgtagtttcgtataaaaattattgtcttcatgtctttcatcgatgcagGTTCTTAGCATGGCTTGCTGTATATTTTATAGCCATTGTGGTAATCGAGCTGTTCTGAGGCAAAAACCACTTGGAAGACAGTATACAAGCTGGTTTTCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG