Sequence
atgc intronic sequence ATGC exonic sequencegtgggtacttaaacttatgaattatgatcgattactagattggcatacaacttttttgattcaactctggtatctagatgaatatcctatgcatggatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G00470.1 (Glycine max), 3'ss of exon 3
gtgggtacttaaacttatgaattatgatcgattactagattggcatacaacttttttgattcaactctggtatctagatgaatatcctatgcatggatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
| ||| ||| | || | ||| | | | | || | || || | | | ||| | || ||||||||||||||||||||||||| ||| ||||||| |||||||| | ||||| ||||| ||||| ||| | |||||| | ||||| ||||| || |
------aattatactattttatctctgtatcttattctcatcctcaggagcattgtaagttttgcttgaatgacctgtatcttatttcactttgactgctgtgcagGAATATGATGTTGAGGACTCTATCTTGCCACTTCAACCATCACTTAATTACACTGCTCCTGAGCTGGCGAGGAGCACTGCGTCTTCAGCTGGGTGCTCAT
upper sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G37070.1 (Glycine max), 3'ss of exon 3
----gtgggtacttaaacttatgaattatgatcgattactagattggcatacaacttttttgattcaactctggtatctagatgaatatcctatgcatggatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
| ||| | | |||| || | || || || || | | | || ||||| |||| | || | ||||||||||||||||||||||| || ||||||| || ||||| | ||||| ||||| ||||| ||||| |||||| ||||||||||| || |
aactatactattttatgtctgtatcttattctcatcctcaggagcaaagtaagttttgcttaaatgacct---gtatc-------atatttcactttgactgctgtacagGAATATGATGTTGAGGACTCTATTTTGCCACTTCAGCCATCACTTAATTACACTGCTCCTGAGCTGGTGAGGAGCACTGTGTCTTCGGCTGGGTGCTCAT
upper sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 3
gtgggtacttaaacttatgaattatgatcgattactagattggcatacaacttttttgattcaactctggtatctagatgaatatcctatgcatg-gatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
| | | || | || | |||| || | | || || || | || | || | | | || || | || |||||||||||||||||||||| ||||| ||||| || || ||| | | ||||| ||||| |||||| |||| ||||| | | ||| | |||||| | |||
-------atcatatccttgcactagagatttctttattattgtgttagagaatgttatatccatgaattgtctggctattatttcctgatcaatttggcctgtgcagGAATATGATGTTGAGGATTCAATACTGCCCCTTCAGCCAGCACTGAATTACACTGCTCCTGAACTGGTTCGGAGTAGAGGATCTCCAGCTGGATCTGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttgattcaactctggtatctagatgaatatcctatgcatggatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
ttttgat putative branch site (score: 4)
atgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtacttaaacttatgaattatgatcgattactagattggcatacaacttttttgattcaactctggtatctagatgaatatcctatgcatggatctatgcagGAATATGATGTTGAGGACTCAATCCTGCCACTCCAACCATCTTTAAATTATACTGCACCTGAATTGGTGCGGAGCAAAACTTCTTCGGCTGGAGTTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA