Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaagatttctttctgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43230.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g67340.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------gtaagaaagatttctttctgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
| | | | | | | |||| | | || | ||| | || | ||||| || |||||| ||||| || |||||||| ||||||||||||||| ||||||| |||||||||||||| || | || |||||||| || |||||| | ||||| ||||
gtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgt--aacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
upper sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 3'ss of exon 4
-------------------------------gtaagaaagatttctttctgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
| | || ||| | | | | |||| | || | | || | | |||| | ||| |||||||| || | || ||||||||||| ||| ||||||| |||||||| ||||| || |||| ||||||| |||||||| ||||||| | ||
ttaagttggttgcctgtttcttttgtaataactcaaaataattcatatatagcagtgctctgatattgtttttgttt----ttcacatccttgtcatacataagGAAGAAAGGGTGTCCCTGGTGCACAACCTGGCCCAGCACTTGACTGGATGCAGCGAGTGAGAATTGCTATTGATGCTGCTAAAGGGCTAGAATATCTTCA
upper sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 5
----gtaagaaagatttctttctgctcaaacat---caatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
||| | | || ||| | ||| | |||| | || ||| | ||| ||| |||| ||||||||||| ||||| || |||||||| ||||| ||||| ||||| || ||||| || |||| ||||||||||| | ||||| ||||| |||||
gtatgtagcttcgtgtcctatcttgtatttcatatctattatgttccgtcaatgattttggttgtctttccacta--cagGTAGAAAGGGAGTTCAAGGTGCTCAACCTGGGCCAACTCTTGATTGGATACAGCGAGTTAGAATTGCAGTTGATGCAGCAAGGGGATTGGAATATTTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
attgataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaagatttctttctgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT