Sequence
atgc intronic sequence ATGC exonic sequencegtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaactaatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18830.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g33810.1 (Oryza sativa), 3'ss of exon 4
gtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaact-aatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
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-----gtatataaccaggctcta-agtttctcaatagcacgctgttttcatgcccaaaagattgttctgaactcaatgccatacg------taaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT
upper sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G109354_T01 (Zea mays), 3'ss of exon 4
gtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaactaatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
|| ||| | || || ||| || || || | |||| | | ||| ||| || || ||||| ||||||| || ||||||||| | |||||||||||| |||||||||| || || || || |||| ||||| ||||| ||||| ||||||||| || |||||
--------------------gtatagtct--tgctctaagttcat-ttaacat----agaaccatattattttaaagggatgctat--atgtgaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT
upper sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G28460.1 (Glycine max), 3'ss of exon 4
gtattctcaagaattatatattacagtttagtgttcaaa----gactatgtttaccttctcagaatctcaaagaactaat-atcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
||||| | ||| ||| | |||| ||||||||| || || | | | | | | | | | | | |||| || | | || || | | ||||||||||||| ||||||||||| | |||||||| ||| ||||||| ||||||||||| || ||||| || |||| | ||||| |||||||| | || ||||
gtattttaaagcattgt-tattgcagtttagtatttgaatagtggcaagatcttctaccgtatacatgctagtaactgattaacaggctgccaaat-gcatttgcagATATTCCAATGGTTGGCAAGTATGCCTGTGGAGTTGGAGGGATATATCCGCCCTGGGTGTACGATCCTGACAATTTTTATTGCAATGCCTAACATCATGT
upper sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G10620.1 (Glycine max), 3'ss of exon 4
gtattctcaagaattatatattacagtttagtgttcaaagact---atgtttaccttctcagaatct-caaagaactaat-atcttgcgattaatttgaatt-tgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
||||| | ||| ||| | |||| ||||||||| || || | | | | | || || | | | | |||| || | | || |||| | || |||||||||| ||||||||||| || |||||||| || |||| || ||||||||||| || ||||| || |||| || ||||| |||||||| | |||||||
gtattttaaagcattgt-tattgcagtttagtatttgaatagtggcaagatcttctgctatgtacatgtatgtaactgattaacaggcagccaattgcatttgtgcagATATTCCAATGGTTGGCAAATATGCCTGTAGAATTGGAAGGATATATCCGCCCTGGGTGTACGATCCTGACAGTTTTTATTGCAATGCCTAACATTATGT
upper sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g02160.t01 (Vitis vinifera), 3'ss of exon 4
gtattctcaagaattatatattacagtttagtgttcaaa-gactatgtttaccttc-----tcagaatctcaaagaac-taatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
||||| | ||| ||||| |||||||||||||| || | | || || | || ||||| | | ||| || || | | | | | | ||| ||||| || || |||||||| | ||||||| ||||| |||||||||||||||| || || |||| || || || | ||||| ||||||||| || ||||||
gtattttaaaggattat-tattacagtttagtatttatatgagaataaatgtttttataagtcagagataccaggaatatattaacacactgctcaat-gtgtttacagATTTTCCAGTGGTTGGCTAGCATGCCTATTGAGTTGGAGGGCTATATCCGTCCTGGGTGTATCATCTTAACAATTTTTATTGCAATGCCAAAGTTTATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaccttctcagaatctcaaagaactaatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
attaatttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaactaatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG