Sequence
atgc intronic sequence ATGC exonic sequencegtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttgaaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G011912_T01 (Zea mays), 3'ss of exon 1
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatca-gcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttgaaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
|||||| ||| | ||| || | | | | ||| | || | || | ||||| | | || |||||| | | ||| | |||| || ||| | |||||| || |||||||||||||| || || ||| |||| |||| | |||||||||| |||||||| | || || |||| |||||
-----------------------------------------ctgaattatttttactgtcttctcgaaaactacataactgaagattccaatgctatgtaattgataacatgacaatcaa------tctctattatcttattc----------acagTTACTGGTGCGTTCAACATTGGTATTTTTCATTGGCGACCCACTGAACCTGCTAAAAGGCTGGCAAAAGATTGGAAAGATTTAGTCATATCTGATGATAA
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G09650.1 (Glycine max), 3'ss of exon 3
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttg-aaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
||||| | | | | ||| ||| | || || ||| | || | | | | | | | | | | ||| || ||| | |||||||||||| ||||||||||||||||| |||||| | || ||||| ||||||||||| || ||||| |||||||| ||| | || ||||||| |||||
------------------------------------------------------tcacttctttatctttatctctcattttgtat-agcatca--caatttcttagctttaatggaagagatacttattgatgattgtgtctatcaccttgtatagTTGGTGCTGCTTACAACATAGGAATTTTCCATTGGAGACCTACAGAGTCTGCGAAAAAATTAGCAAAGGAATGGAAGGAACTGCTTCTAGCTGATGATAA
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G20730.1 (Glycine max), 3'ss of exon 5
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttgaa-agTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
|| || | | | | | | | ||| | | || | ||||| | | | ||||| | | | |||| ||| || ||||| |||| ||| || ||||||||||||||||| |||||| | || ||||| ||||| ||||| |||||||| ||||||||||||| ||| ||||||| || |
-----------------------------------------------------ttctcttacctattgtttctcttcatctctcatt-tattctgcatacggtttcacgttatt-ttgactgtatatt--gatgatcttgtctatcaccttgaatagTTAGTGGCGCATACAACATAGGAATTTTCCATTGGAGACCTACAGAGTCTGCAAAAAAATTGGCAAAGCAATGGAAAGAAATGCTCCTAGCTGATGACCA
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08350.2 (Glycine max), 3'ss of exon 4
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttgaa-agTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
||| ||| | | | || |||||||| || || |||| | | | ||||| | | | |||| ||| || ||||| |||| ||| || ||||||||||||||||| |||||| | || ||||| ||||| ||||| |||||||| ||||||||||||| ||| ||||||| || |
----------------------------------------------ttctcttacctattgtttctcttcatctttcatttattat--------gcatattgtttcatgttatt-ttgactgtatatt--gatgatcttgtctatcaccttgaatagTTAGTGGCGCATACAACATAGGAATTTTCCATTGGAGACCTACAGAGTCTGCAAAAAAATTGGCAAAGCAATGGAAAGAAATGCTCCTAGCTGATGACCA
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 5
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttg-aaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
|||| || || | | | | || || || ||| | ||| | || | | | |||| | || || | | || || ||| | |||||||||||| |||||||| |||||||| |||||| | || || || ||||||||||| || ||||| |||||||| ||| | || ||||||| |||||
-------------------------------------------caatttcttagctttaacggaagagatactatg--ttgatgattgt---------gtctat---cacctttttttttttttttttttaaacttgtgtcctatcaccttgtatagTTGGTGCTGCTTACAACATTGGAATTTTCCATTGGAGACCTACTGAGTCTGCGAAAAAATTAGCAAAGGAATGGAAGGAACTGCTTCTAGCTGATGATAA
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 5
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccg------ttcttttcttggactttgaaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
| || ||||| ||||| || | | | | | || || ||| || | || | |||||| ||| || | |||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| ||||| ||||||| ||| |||||||| || || ||||||| |||||
-------------------------------------------------------------aatgatgaagtagtgagtg-attatctccattaattgcttggctgctatttcttttaaatgatcatcctgctaatgagattctttctttgcttcttaacagTTGGTGCTGCCTACAATATAGGAATTTTCCACTGGCGACCAACAGATTCTGCAAAAAAATTGGCAAGAGAGTGGAAAGAGATGCTTCTAGCTGATGATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcacatggctactaactgttttctctaccgttcttttcttggactttgaaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
tactaac putative branch site (score: 0)
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatgttagctatagatatgcattttcccctgttcccatttgaattcgtttatcactctggcaaaagtgttttgagtttattattatcagcagctaatctgttcacatggctactaactgttttctctaccgttcttttcttggactttgaaagTTGGTGCTGCCTACAACATAGGAATTTTTCATTGGCGGCCGACAGAATCTGCGAAAAAGTTGGCAAAAGAATGGAAAGAAATTCTCTTAGCTGACGATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA