Sequence
atgc intronic sequence ATGC exonic sequencegtgtgctaattacatactttcgttgtgaattgtgattaaagaaatcctactagaaaccaaatttactaatggagacacttgttcattttgtagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26780.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 5
----gtgtgctaattacat-actttcgttgtgaattgtgattaaagaaatcctactagaaaccaaatttactaatggagacacttgttca------ttttgtagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
| || || || | |||| | || | | || |||| | || | || || || | ||||| ||| |||||||||||| || ||||| ||||| || |||| ||||||||||||||||| || ||||| |||||||| ||||| |||||||||||| | || |||||
gttcatatgtcttttctattattttcctccacaacttgggggaacaaaatttt----gagaatgtgctttcttggagaatcttatgttctctgctttttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG
upper sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 5
----gtgtgctaattacat-actttcgttgtgaattgtgattaaagaaatcctactag-aaaccaaatttactaatggagacacttgttcattttg-tagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
| || || || | |||| | | | | || |||| | || | || ||| | | ||||||| |||||||||||| || ||||| ||||| || |||| ||||||||||||||||| || ||||| |||||||| ||||| |||||||||||| | || |||||
gttcatatgtcttttctattattttcctccacagcttgggggaacaaaattttgataatgtgctttcttggagaatcttatgttctctgcattttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG
upper sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
-gtgtgctaattacatactttcgttgtgaattgtgattaaagaaa--tcctactagaaaccaaatttactaatgg---agacacttgttcattttg-tagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
||| ||| | || | | | |||||| | | | || | ||||| |||| | | | | | || || ||||| ||||||||||||||| ||||| ||||| || || || || |||| |||||| ||||| || || |||||||| |||||||||||||||||| | ||||||||
tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
upper sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgctaattacatactttcgttgtgaattgtgattaaagaaatcctactagaaaccaaatttactaatggagacacttgttcattttgtagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
| | || || | ||| ||| | |||| || |||| ||||||||||||||| ||||| || || ||||| || || ||||| || || || ||| | || || || |||||||| ||||| |||||||||||||| ||
---------------------------------------gtacgttttatcagtggcgaaa--ggataaagctctgacttcttttctttgcagTCAATGTGCAGTCATTATCTGGTTCTCCAGCAAACTTTCAAGTGTATACAGCTTTGCTTAAACCACACGAAAGAATTATGGCTCTTGATTTACCTCACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaaatcctactagaaaccaaatttactaatggagacacttgttcattttgtagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
tactaat putative branch site (score: 1)
ttcatttt putative PPT
aaatttactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgctaattacatactttcgttgtgaattgtgattaaagaaatcctactagaaaccaaatttactaatggagacacttgttcattttgtagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA