Sequence
atgc intronic sequence ATGC exonic sequencegtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 18
-gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
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gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtccatt-tacaccattat-tgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
-gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
| || | | ||| |||| | | | | | ||| | || | || || | | | ||||| ||||||||||| |||||||||||||| || ||||||||| |||||||||||||||| || |||||||||| || ||||| ||||| || || |||
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatt-tacaccattat-tgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
| | || | | || ||| || || | || || ||||| ||||| | || | ||||| ||||||||||| |||||||| ||||| || |||||||| | |||||||||||||| || | ||||| || ||||| || ||||| ||||| |||
-----gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttcttgtttattaacaacttcct---tgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 17
-----------gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
| ||| | | ||| ||| | |||| | | | ||| | || | || | || | || ||||| | || ||||| |||||||| ||||| || | || ||||| | ||||||||||| ||||| ||||||||||| || |||||||| || ||||| ||||
gtttgtgtgttccattgcttttataatttatct--attgtaacatcatgctagttttaaaatacttagtcattgttcggttct---tgcagTCACTCGTTGAATTTTTTGGTACTCTGTCACGAGAATGGGCATTAGAGTGCATGAAAGATCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
gtagtgcctctgaaatatattttggttgttaaacctactaagtggtc---aagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
| | | | | | | ||| | |||| | ||| || ||| | || || | || | | ||||| ||||| ||||| ||||| || ||||| | || |||||| |||||||||||||||| || | |||||||| || |||||||| || ||||||||||
-----gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttc--tcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
gcataac putative branch site (score: 3)
ctctgctcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT