Sequence
atgc intronic sequence ATGC exonic sequencegtatgattcttattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03190.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 8
------gtatgattcttattttatgatctta---ttagat--tttggtgtgcaactcttttacctgtttgtgac----tgttgttaactcttt---ttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
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gtaataatactacttctgccaggggaaagtagggctggatgatttgtagctttatttttctagagacatccaacaaagttttcttgacattttggattctgttaatgccagAGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 3
-------------------------gtatgattcttattttatga----tcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaaca-cagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
|| | || | || ||| |||||| || || ||| | | ||| | | | || | | | |||| ||||||||||| || |||||||| || || || || || || || |||||||||||||||||||||||||| ||||| ||
gtaattcattattactttgaggaaaaaataactccttttgattgacacctcttatctccttatgttgtcgagatatttgtaacacaatttctcgaaataaatttgaaatctcattaatgtcagAGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
gtatgattcttattttatgatcttat-tagattttggtgtgcaactcttttacctgtttgtgactgtt-----gttaactctttttggcttta-----acacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
|| ||| ||| | | | | | | | | | | | ||||| || | | || || | | | | |||| | ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||||| |||||||| ||||||||||||||
gtttgactctctctctctctctctgtctctctctctatctctatctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
gtatgattcttattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
|| ||| ||| | | | || | | | | || | || | | | | | || ||| ||| || |||| ||||| ||||| ||||| ||||| || || || ||||| ||||||||||||||||| |||||||| ||||||||||||||
gtttgactctctctctctcatataaattactgctgat----aatttgatcatcag---------attcctaaacttttctg--cttaa-gcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
-------------------gtatgattct-tattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactcttttt----ggctttaaca---cagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
|| | ||| | |||| | || | |||||| | | | | | || || | | | | | || || | | ||| ||||||||||| || |||||||| || ||||||||||| |||||||| ||||||||||||||||| || || ||||||||
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgctt--aaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ08988 (Selaginella moellendorffii), 3'ss of exon 8
gtatgattcttattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
|||| | ||||| | | || | | | || ||| | | || ||||| ||||| |||||||| ||||| || || || || ||||| || ||||| || |||||||||||||||||||| ||
---------------------------------------gcaagttctttacgt---tctgttctccgcttattcgttt--acctgtac-cagAGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
ctctttttggcttt CT-rich tract
tctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattcttattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT