Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgttttctgatcttatataaatctcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06290.1 |
intron # | 12 |
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 12
lower sequence: GRMZM2G429213_T01 (Zea mays), 3'ss of exon 5
-gtttgt-gttttctgatcttatataaatctcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
||||| | | | || | || | || || | || || ||| | | || | |||| || ||| | ||||| || || ||||| ||||| |||||||| |||||||||| | |||||||| || ||||| ||||| |||||||||||||| || |||||||||||||
attttgtcatgtgtttatttcat-cagccactatgaatttattctgtgggcacccttatttcctgga-atgtttcatcttgaagctgtcttttgttgagcagATAAGGCTCCACATAATTGCGATGCATGAATTATGTGAATACAACAAAGGAGAAGGTTTTTCCGAGGGTTTTGATGCACACCTCAACATTGAGCAGATGA
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G429231_T02 (Zea mays), 3'ss of exon 5
gtttgtgttttctgatc-ttatataaatc-tcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
|||| ||| | || | || || | | || || | || || ||| | | || | |||| || ||| | ||||| || || ||||| ||||| |||||||| |||||||||| | |||||||| || ||||| ||||| |||||||||||||| || |||||||||||||
gttt-tgtcatgtgtttatttcatcagccactatgaatttattctgtgggcacccttatttcctgga-atgtttcatcttgaagctgtcttttgttgagcagATAAGGCTCCACATAATTGCGATGCATGAATTATGTGAATACAACAAAGGAGAAGGTTTTTCCGAGGGTTTTGATGCACACCTCAACATTGAGCAGATGA
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G429231_T01 (Zea mays), 3'ss of exon 14
gtttgtgttttctgatc-ttatataaatc-tcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
|||| ||| | || | || || | | || || | || || ||| | | || | |||| || ||| | ||||| || || ||||| ||||| |||||||| |||||||||| | |||||||| || ||| | ||||| |||||||||||||| || |||||||||||||
gttt-tgtcatgtgtttatttcatcagccactatgaatttattctgtgggcacccttatttcctgga-atgtttcatcttgaagctgtcttttgttgagcagATAAGGCTCCACATAATTGCGATGCATGAATTATGTGAATACAACAAAGGAGAAGGTTTTCCCGAGGGTTTTGATGCACACCTCAACATTGAGCAGATGA
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G28300.1 (Glycine max), 3'ss of exon 6
gtttgtgttttctgatcttatataaatctcat-taaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctg-ttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
| | | || || | | || | | || || || ||| | | | | | || ||||||| || || ||||| | | | || ||||||||||||||||| |||||||||| ||||||||||| || ||||| ||||| |||||||| || || |||||||| |||||||
--aaagagcagttagtttaatctagaacatgcatatgcttgttgccaagcagtatctgatgattgcaaaggctaatgaagctgttgatttctgtggtttcagATAAAATTACATATCATTGCAATGCATGAATTATGTGAATACACTAAAGGAGAAGGATTTTCCGAGGGCTTTGATGCTCATCTCAATATTGAACAGATGA
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G10760.2 (Glycine max), 3'ss of exon 4
--gtttgtgttttctgatcttatataaatctcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctg-ttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
|| |||||| || | |||| || | ||| | | || || || ||| | | | | | | || ||||||| || || ||||| | | | || ||||||||||||||||| |||||||||| ||||||||||| || ||||| ||||| |||||||| || || |||||||| |||||||
aatttggtgtttatcaatttcatatttatat-attg--cttgttgcaaagcagtatctggtgattacaaaggctaatgaagctgttgatttctgtggtttcagATAAAATTACATATCATTGCAATGCATGAATTATGTGAATACACTAAAGGAGAAGGATTTTCTGAGGGCTTTGATGCTCATCTCAATATTGAACAGATGA
upper sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0020g02350.t01 (Vitis vinifera), 3'ss of exon 7
-----gtttgtgttttctgatcttatataaatctcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
| | | | | | | | | ||| | | || || | | | ||||| | | | | || ||| | | || ||||| |||||||| || || || |||||||| |||||||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||
ctactgctggaggatac-gcgttagtctaagtgatgtgttccaaagtgtcatatga--ttcttctcaagactaagagagttttctgatt--tctgtgggtgccagATAAGACTTCATATAATAGCCATGCATGAATTATGTGAATACACAAAAGGAGAGGGATTTTCTGAGGGATTTGATGCACACCTCAATATTGAGCAGATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
ttttcctgtt CT-rich tract
atattcttttttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgttttctgatcttatataaatctcattaaacaggatgataaacaatattcttttttaaatgcgtgtgttcttactattgattttcctgttacagATTAGACTTCACATCATTGCAATGCATGAGCTATGTGAATATACTAAAGGAGAGGGCTTTTCGGAGGGGTTTGATGCACACCTGAATATTGAGCAGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG