Sequence
atgc intronic sequence ATGC exonic sequencegttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18040.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 5
gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
|| ||| | ||||| | ||| ||| | ||| | || | ||||||| | || | | | | | | |||| | ||||||| ||||| ||| ||||||| || || ||||| | ||||| || | |||||||||||||||||||| |||||||||
----------gtaggaatgtagctactagccagcatagagcaattgctcaaaaatgttattctaatattcgttatc-----cattatactgatat-tatagttatgtgtcaagGCCTTAACAGATCCATACTTTACTGGATTGGCAAATTCGGAACGTGAACCCATAGCACAACCCATCTCAAAACTCGAGTTTGAGTTTGAGAGAAGGAAGC
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
|| ||| | || | | ||||||| | ||| | || ||| | |||||| | | ||| |||| |||| |||||| | | |||||||||||| ||| |||| ||| | || || |||||||| |||||||| ||| | ||||| |||||||| ||||| ||||||||
-------------------gttaatctcctatcacctatatataatttcattga-----taattac-ctaagagtatatttcattatttctgt-catgtttgtg-atat-cagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 6
gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
|| ||| | || | | ||||||| | ||| | || ||| | |||||| | | ||| |||| |||| |||||| | | |||||||||||| ||| |||| ||| | || || |||||||| |||||||| ||| | ||||| |||||||| ||||| ||||||||
-------------------gttgatctcctatcacctatatataatttcattga-----taattac-ctaagagtatatttcattatttctgt-catgtttgtg-atat-cagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGCGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
-------------gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatat---acagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA----------------------------------------
| | | | | || | | |||| | | | | ||||| || | |||| || ||| || | | | |||| | || |||||||| || ||||| ||| ||| || ||||| ||||| || |||||||| ||| | ||||| |||||||||||||| ||||||||
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 6
------gttagctcctcta-tacttgttttttctagcgtttccacttcaaaatttcagagcagt----ttcaatcgctctcagaaaaggaaacattata-tatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
||| | |||| || || | | | ||| | | |||||| | || | | | | | | | | ||| | | | || ||| || |||| | | | ||||| | || ||||| || || ||||| ||||||| || ||||| ||||| || |||||||| ||| | ||||| |||||||||||||| ||||||||
gtaatagttggtaattctaatatttcgctacttcaaaatttaaatt--aaaattgtaaagaaatataatctagttgatttgggaacactgtgcttcctaatatcattgcgtgtttatgttggcagGCTTTAGCTGATCCGTATTTTGATGGTTTGGCAAATGTAGATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAAT
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------gttagctcctctatacttgttttttctagcgtttccact----tcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
| | | | | || |||| | |||| | | || | || ||| | | ||| || | | | || ||| || | | | | | | |||| ||||||||||||| ||| | ||| ||||||| || ||| ||||||| ||| ||||||| ||| ||||| | |||||||||||||||||||||| |
gtacctcatggattgtacaacatgggatcgaatacagttaaatgcatgtttggacgattttgaagttcttttcaaagtcttttctgttattcttaatggaactgaattccttcttttgtagtcataatatgtcgctttgtatctaaac-tatattgatgggtgtagGCTTTGGCAGATCCTTATTTCAAAGGTTTGGCAAAAGTGGATAGGGAACCCTCTGCTCAACCAATTACGAAAATGGAGTTTGAGTTTGAAAGAAGGAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
aaacattatatataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA