Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttctcgatctctctttctccatggatctgtggatagatagatgtatttgtgtgtggaaatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29810.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29810.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G16650.3 (Glycine max), 3'ss of exon 1
gtatgtttctcgatctctctttctccatggatctgtggatagatagatgtatttgtgtgtgga-aatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCA-ATTG-----------
|| ||||| |||||| || | | ||| | | | ||||| | || |||| || | |||| | |||||| | | | ||||| | ||||||||| |||| || || ||||||||||| ||||| | ||| |||| ||||||||||||||| | ||||| | ||
--gtgagtctcgccctctctctccctctctctctctctctttgt-gatgtgtgtgaatgtgattgattaattatgtttggcttttgagccaattgaattattggta---tgtgtagGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT
upper sequence: AT4G29810.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G16650.2 (Glycine max), 3'ss of exon 1
----gtatgtttctcgatctctctttctccatggatctgtggatagatagatgtatttgtgtgtgga-aatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCA-ATTG-----------
| || ||||| |||||| || | | ||| | | | ||||| | || |||| || | |||| | |||||| | | | ||||| | ||||||||| |||| || || ||||||||||| ||||| | ||| |||| ||||||||||||||| | ||||| | ||
gttcctgtgagtctcgccctctctctccctctctctctctctctttgt-gatgtgtgtgaatgtgattgattaattatgtttggcttttgagccaattgaattattggta---tgtgtagGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT
upper sequence: AT4G29810.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G06020.1 (Glycine max), 3'ss of exon 1
gtatgtttctcgatctctctttctccatg-gatctgtggatagatagatgtatttgtgtgtggaaatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCA-ATTG-----------
| ||||||| | || || ||| |||| | |||| ||| | || | | |||| | |||||| | | | ||||| | ||||||| |||| || || ||||||||||| ||||| | ||| |||| ||||||||||||||| | ||||| | ||
--------gtgagtctctctctttctttgtgatgtgtg------tgaatgtgattgatt----aattat-----gtttggcttttgaccaaattgaattgttggtatt-----tagGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggatagatagatgtatttgtgtgtggaaatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCAATTG
ttttgttttt CT-rich tract
ttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttctcgatctctctttctccatggatctgtggatagatagatgtatttgtgtgtggaaatgtctctggttttgtttttgaagGAGGAAAGGTTTTGGTTCTCTCTGTAGGACTCAAAGCGGTACGTTTAAGGATGGAGATCTACGTGTTAACAAGGATGGAGTTCGAATCATTTCTCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA