Sequence
atgc intronic sequence ATGC exonic sequencegtctgtttacctgatctgtattagtctcctttttttcagaaaatgaatagctaactgaatgtatattctcttattttctttgcacagCATTCACTGCGTGATGGTAAAAGGTGAGAATTTGTTGAATGGTGAATGCACAAAGAGCAAACTATGGTTAGTTGATTTAGCAGGAAGCGAACGGGTTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72250.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G18590.1 (Glycine max), 3'ss of exon 12
---------------------------gtctgtttacctgatctgtattagtctcct--ttttttcagaaaatgaatagctaactgaatgtatattctcttattttctttgcacagCATTCACTGCGTGATGGTAAAAGGTGAGAATTTGTTGAATGGTGAATGCACAAAGAGCAAACTATGGTTAGTTGATTTAGCAGGAAGCGAACGGGTTGCT
| | ||| || || ||||| | || | | ||| | ||| | ||| || || || ||| || | ||||||||||||| || ||||| || || ||||||||||||||||| |||||||||| ||||| ||||| | || || ||||||| ||||| || || ||
gtgaatttaaacttttttttttattagattcctgaaccatatgtgaattaggtttctaaaccatctggttggagaaaaactactt--atg-atgggctattgttt-ctctatacagCATTCACTGTGTTATGGTTAAGGGAGAGAATTTGTTGAATGGGGAATGCACAAGAAGCAAGTTATGGCTGGTGGACCTAGCAGGCAGCGAGCGAGTGGCA
upper sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G40350.1 (Glycine max), 3'ss of exon 12
-------------------gtctgtttacctgatctgtattagtctcctttttttcagaaaa-tgaatagctaactga-atgtatattctcttatt--ttctttgcacagCATTCACTGCGTGATGGTAAAAGGTGAGAATTTGTTGAATGGTGAATGCACAAAGAGCAAACTATGGTTAGTTGATTTAGCAGGAAGCGAACGGGTTGCT
| | ||| | | |||| | || | ||| | | | || | | ||| ||| | | | || |||| | ||||||||||||| || ||||| || || ||||||||||||||||| |||||||| | ||||| |||||| | || || ||||||| || || || || ||
gtcagcttaaactttttttaattagattcctaaaccatatttgaatcatatttctaaaccatctggttggataaacaccgcttatgatggcctgttgtttctgtatacagCATTCACTGTGTTATGGTTAAGGGGGAGAATTTGTTGAATGGGGAATGCACGAGAAGCAAGCTATGGCTGGTGGACCTAGCAGGCAGTGAGCGAGTAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcagaaaatgaatagctaactgaatgtatattctcttattttctttgcacagCATTCACTGCGTGATGGTAAAAGGTGAGAATTTGTTGAATGGTGAATGCACAAAGAGCAAACTATGGTTAGTTGATTTAGCAGGAAGCGAACGGGTTGCT
agctaac putative branch site (score: 2)
tattctcttattttct putative PPT
tatattctcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtttacctgatctgtattagtctcctttttttcagaaaatgaatagctaactgaatgtatattctcttattttctttgcacagCATTCACTGCGTGATGGTAAAAGGTGAGAATTTGTTGAATGGTGAATGCACAAAGAGCAAACTATGGTTAGTTGATTTAGCAGGAAGCGAACGGGTTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA