Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgtactggccaaccaagtctgttattactctattgtttttgttggattagatttcatatgattccaagtttatattcagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03070.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------------------------gtttgttgtactggccaaccaagtctgt---tattactctattgtttttgttgga-ttagatttcatatgattccaag---------------tttatatt---cagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
|| || | || || | || ||| |||| |||| | ||| ||| | | ||| | | || | || ||| || ||||||||||||| ||| || || ||||| || |||||||| |||||||||||||| |||||||||| ||| |||||| | | | ||||| ||
gttagtttcatctctcttgttggttgaaattaaataattttcttcaatgctcatcttcattcccattaggaagatattgctatatgttcctgtatgcgtttctcaagaatgatgtttgtagatatttttctactatttagtttgaaatcagagctttgactatgctaaaaatttaattgagctacctatgttggttagAAAAGAGCTCCACACTTGTTGCCGAGCAATGTGCATGGGCCATTGGTAATGTTGCTGGTGAAGGAGCAGAGCTGAGAAGCACATTACTTGCACAAGGTGC
upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------gtttgtt-gtactggccaaccaagtctgttattactctattgtttttgttggattagatttc-atatgattccaagttt---atat---tcagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
| || | | | | | | |||| | | | | | | || | | ||| | || | || || | | ||| || ||||| ||| || || || || || |||||||| |||||||||||||| |||||||||| ||| ||||||| | | ||||||| ||
gttagttttcttttatttgttggtcaaatgtacatattgtccatttccattcacattaatctccagaatacacaattatta-agaatggctactaggttgacctcctatagaagtcttatcttcctatgtctgttagAGAACAGCTCTACACTTGTCGCGGAACAATGTGCATGGGCCATTGGTAATGTTGCTGGTGAAGGAGCAGAGCTGAGAAACACATTACTTGCTCAAGGTGC
upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g02290.t01 (Vitis vinifera), 3'ss of exon 4
--------gtttgttgtactggccaaccaagtctgttattactc--tatt--gtttttgttggattagatttcatatgattccaagtttatatt---cagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
||| || | | || || | ||| | ||| | | || || | | ||| || || | | |||| ||||||||| ||| | || || ||||||||||| |||||||| | || |||||||| ||||||||||| || |||||||| |||| | || ||||| ||
aaaatggagttaattttggagagggacagggtttagggttattaagcattaggatctttctgactctggttttgcatttttaaatgcacttattgtgtagAAAAGAGTTCCCCTCCTGTTGCTGAGCAGTGTGCATGGGCGTTGGGAAATGTTGCTGGTGAAGGAGAGGAGCTGAGAAATATTCTACTATCACAAGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactctattgtttttgttggattagatttcatatgattccaagtttatattcagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
attagatttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgtactggccaaccaagtctgttattactctattgtttttgttggattagatttcatatgattccaagtttatattcagAAAAGAGCTCCGCACCGGTGGCTGAGCAGTGCGCATGGGCAATTGGTAATGTTGCCGGTGAAGGAGAAGATTTGAGAAATGTTCTTTTGTCTCAAGGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA