Sequence
atgc intronic sequence ATGC exonic sequence...gatctactgactctattgtttaacatagttgcacacctatcaatgggtgtttcgtggacaactctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
gatctactgactcta-ttgtttaacatagttg-cacacctatcaatgggtgttt-cgtggacaactctctttatttattttcggacaattttcgactt---gttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
| | | || | || | ||| | | | | ||| | | | | | | | | | | || | ||| | || || | |||||| ||||||||| | || ||||| || ||||| ||||||||||| ||| | || || || ||||| ||||||||||| | | ||||| || || | |
----tgtttattcaaatttcagagttcagtcatcggatttgaagtttggtaatagtggtaatatattacctgaatcctaatcaaa--attcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
gatctact--gactctattgtttaacatagttgcacacctatcaatgggtgtttcgtg--gaca-actctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
| || | | | | ||| | | | | || | || || ||| | | | | || || | | | || || |||||| |||||||| |||| ||||| || ||||| |||||||| || ||| | || || || ||||||||||||||||| | || ||||| || || | |
-gtttattcaaatttcagagttcagt----cttcggatctgaagttttgtaattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 17
-gatctactgactctattgtttaacatagttgcacacctatcaatgggtgtttcgtggacaactctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
|| | | | | ||| | |||| | | | | || || | | | | | | || || ||||| |||||| |||| ||||||||| | || || ||| | || ||||| |||||| |||| |||||||||||||| |||||||| | || ||||| || || |||
tgaccgcattttttttccacttattcttgttgtttcaattcctttttccatagttctga-aatttgactgagatgtgatgaagatatattttacttgctagTGTGGCTCGTTTCTTGGAAGCTCGAGGTATGCTGGAGGATGCACTGGAAGTTGCCACAGATCCTGACTATAGATTTGATCTAGCTATACAGCTAGGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgtttcgtggacaactctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
tctctttatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatctactgactctattgtttaacatagttgcacacctatcaatgggtgtttcgtggacaactctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
- - - - - - - - - - -aacatag
- - - - - - - - - - - - - - - gcacacc