Sequence
atgc intronic sequence ATGC exonic sequencegtagttccttggatttttttgttggctgttagttttttaacttgatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06290.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G28300.1 (Glycine max), 3'ss of exon 8
gtagttcct-tgga--tt--tttttgttggctgttagttttttaactt---gatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
||| ||||| | || || |||||||| | || | || | | || ||||| | ||| | || | | |||||| ||| |||| || || || || ||||||||||| |||||| | ||||||| |||||||||||||| |||||||||||||| ||||| ||
gtaattcctatagaagttagtttttgtttcttttttggttatcatgtttgtgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACAGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTTCTAAG
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G10760.2 (Glycine max), 3'ss of exon 6
---gtagttcct-tgga--tt--tttttgttggctgttagttttttaactt---gatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
| | ||||| | || || |||||||| | || | || | | || ||||| | ||| | || | | |||||| ||| |||| || || || || ||||||||||| |||||| | ||||||| |||||||||||||| |||||||||||||| ||| | ||
gttgaaattcctgtagaagttagtttttgtttcttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0020g02350.t01 (Vitis vinifera), 3'ss of exon 9
----gtagttccttggatttttttgttggctgttagttttttaacttgatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
| |||| || |||| | | | | || ||| |||| | |||| | | | | ||||||||||||||| | || ||||| || |||||||| |||| ||||||||| |||||||||||||| |||||||||||||| ||| | ||
gtttgcctccccttaaatccacttgtcaggt-tgaagcattgaacagaatctca-tattagagtgattgtcttcatgcagAGCTTGCAGAACAAGTAATTTCATTGCTTTCTTTCGGCTTGGGAAGAAAGCAAGTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S55_70V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------gtagttccttggatttttttgttggctgttagttttttaacttgatctaagtat-tgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
| || ||| | | | || | | | | | || || || | | ||| || ||| | || || | || || || || || | || |||| || | ||||||||||||||||| ||||||||||||||||||||
ctcttgtgctctcgcactaatgcacactttcttagcagacatgaatatttgatggaaagatttttccgcttgggtgggtgtgttcaactggatttatcagGGCATGCCGTGGGGGTAATTATATTGCATTTTTCCGTTTAGCGAGGAAGGCCACATATCTTCAAGCATGTCTCATGCATGCTCATTTTTCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggctgttagttttttaacttgatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
ttagttttttaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttccttggatttttttgttggctgttagttttttaacttgatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT