Sequence
atgc intronic sequence ATGC exonic sequence...aaggaaatctcataactcttttgttccaggatcttgacggcaggagactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36390.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 9
aaggaaatctcataactcttttgttccaggatcttgacggcaggagactttcacttttgacaatat-gataa--tgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
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-tatatgtaccatt-ctattgggtaattgaagtttcagtactataaactatgatcatctatacttcagataaactgagtattttaggtga-tctgttacacagGAACCAAAGATAAATACATATGCTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAAC
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G37750.1 (Glycine max), 3'ss of exon 9
-----aaggaaatctcataactcttttgttccaggatcttgacggcaggagactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
| | | | | | || | ||||| || | || | | | | ||| || | || || | || |||| | | || |||||| ||||| || |||||||||| ||| ||||||||||||||||| || || || |||| ||| |||||||||||||| ||||| ||||| || ||||| |
ttttgtattagagattaaatctatgatgttcaagaaagttcctat--gtatagtatcagttctttttctactatta---acaattttgtgaaccatgcggcgcagGAGCCAAAAATCAATACATATGTCAATTTTAGAGATGATGTACTGCCTCGCATTAAAAGGCTTGGCTATAATGCTGTCCAGATTATGGCTATCCAAGAAC
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 9
aaggaaatctcataactcttttgttccaggatcttgacg-gcaggagactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
| | | | | | || | ||||| || | || | | | ||||| | | | || | || |||| | | || ||||||| ||||| || || ||||||| ||| ||||||||||||||| | || || || |||| ||| |||||||||||||| ||||| ||||| || ||||| |
-attagagattaaatctatgatgttcaagaaagttcctatgtatagtatcagttctttttctacttctactattaacaattttgtgaaccatgtggtgcagGAGCCAAAAATCAACACATATGTCAATTTTAGAGATGATGTATTGCCTCGAATTAAAAGGCTTGGCTATAATGCTGTCCAGATTATGGCTATCCAAGAAC
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 9
---aaggaaatctcataactcttttgttccaggatcttgacggcaggagactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
|||| | | | | || ||| | | | | || | | | | | ||| | | | |||| |||||| || |||| ||| | || |||||||||||||||||||||||||| || || || || |||| ||| || ||||||||||| ||||||||||| ||||| ||||
attggaaaaatttaaatatccaccctacccctcatccttatgctttcaa--ttatgcatagaattttttaatactca-ttttactgttgactttgagatgtagGAGCCAGTAGTCAACACATATGCCAACTTTAGAGATGATGTGCTACCTCGCATCAAAAGGCTTGGTTATAATGCTGTCCAGATAATGGCAATTCAGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
ttatcttt CT-rich tract
aatatgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggaaatctcataactcttttgttccaggatcttgacggcaggagactttcacttttgacaatatgataatgagtaacgttgttatctttgatctgcagGAACCAAAGATAAATACATATGCCAACTTTAGAGATGATGTACTTCCCCGTATAAAAAAGCTAGGCTATAATGCTGTGCAGATAATGGCCATTCAAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
aaggaaa
- - - - - cataact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaata