Sequence
atgc intronic sequence ATGC exonic sequencegtaaacattgagttagaaatctccgtatatgatatgttgcttatgttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G02180.3 (Glycine max), 3'ss of exon 4
--------------------------------------gtaaacattgagttagaaatctccgt--------atatgatatgttgcttat----gttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
| || | || |||| ||| | || | || ||| || ||| || | | ||| ||||| |||||||||| ||| ||| |||||| | || |||||||||||||| ||||||||||||||||| |||||| |||| ||||| || || | || || |||||||
gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgc--attgccttgttt-ggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 4
---------------------------------gtaaacattgagttagaaatctccgt------------atatgatatgttgcttatgttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
| |||| | || |||| ||| | | | | | | | | ||| || | | ||| ||||| ||||||| || ||| ||| |||||| | || ||||||||||| || ||||||||||||||||| |||||| | || ||||| | || || || || |||||||
gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttgatttcattcacaaaacagctcattgagagttttgttgc--attgccttgttt-ggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaaacattgagttagaaatctccgtatatgatatgttgcttatgttt----tccttaccaactgctc---tgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
|| ||| | |||| || | | |||| || | | || || ||||| | | || | || |||||||||||| ||| |||||| | ||||||||||| ||||||||||||||||||||||| ||||| |||| ||||| | || || || ||||||||||
gtaaaattatagatcagttcacactatattagttatggacttttatgctagcccatatgtcttcaggatcaccaccaattaattatttgatctgccagAGTGACAGGTTGCACAAGGTCCTTGAGTTTGTGAGCACTGTTCATGATCTATGTGCTGTCCTTGGGATGGACTTCTTTAATACTGTTACTGAAGTTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctccgtatatgatatgttgcttatgttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
tccttac putative branch site (score: 2)
ctctgtttt putative PPT
tatatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacattgagttagaaatctccgtatatgatatgttgcttatgttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT