Sequence
atgc intronic sequence ATGC exonic sequencegttactcttgtacccatgtgtatgaagtaagaatgacctggagaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 9
----gttactcttgtacccatgtgtatgaagtaagaatgacctggagaacttgaactaattctgcattggtctta-------tgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
||| | | | || || ||| | | | | | | || | | | | | ||| | ||||||||| || || ||||||||||| || |||||| | ||| | |||||| |||||||||||||||| |||||||||| |||||||
gtttgttgtttctagattaataattact--gtagtgccaaattttatacttctacctgtatggaagataatgcaaacaaaattacagTACACTATTGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
-----------gttactcttgtac--ccatgtgtatgaagtaagaatgacctggaga--------acttgaactaattctgcat--tggtc-ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
| ||||| || | | | |||||| || | || | ||| ||| ||| |||| ||| ||| || | ||||||| ||||||||||| || |||||||||||| | ||||||||||||||||| |||||||||||| |||| || |||||||| |
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
---------------gttactcttgtacccatgtgtatgaagtaagaat----gacctggagaacttgaactaattctgcat----tggtc-ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
| | | | | ||| | | | | | | | | | | ||| ||| ||| |||| ||| ||| || | ||||||| ||||||||||| || |||||||| ||| | || |||||||||||||| |||||||||||| |||| || |||||||| |
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 12
---------------------gttactcttgtacccatgtgtatgaagtaagaatgacctggagaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
||||| || | ||| ||| | | | | | || | | | | ||| | ||| | | ||| || | || || | ||||||||||| || || ||||| ||| | ||||||||||||||||| |||||||||||| ||||||| || ||||| |
gtttgcaattttaaactttattttacttttcaattcat-tgttcactctgtgtgtta---gtagctcatctaatcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
----------------gttactcttgtacccatgtg--tatgaagtaagaatgacctgg-agaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
||| | | | ||| | | | | | | || | | | | | | ||| | ||| | | ||| || | || || | ||||||||||| || || ||||| ||| | ||||||||||||||||| |||||||||||| ||||||| || ||||| |
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
gttactcttgtacccatgt---gtatgaag-----taagaatgacctggagaact-tgaactaattctgcattggtc--ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
||| | |||| | ||| | || ||| ||| || | | | || | | | |||| | ||| |||| ||| || | || |||| || || |||||||||||||| || || |||||||| |||||| |||| ||||| ||||| | || ||||| |||||||
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattat-cagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaagtaagaatgacctggagaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
aactaat putative branch site (score: 2)
aactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttactcttgtacccatgtgtatgaagtaagaatgacctggagaacttgaactaattctgcattggtcttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT