Sequence
atgc intronic sequence ATGC exonic sequence...ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgcttattttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07690.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgctt---attttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
| ||||| |||| | | | | | | | | || | | | | | | | | | |||| || ||||||||||||||||| || || |||||||| ||||||||||| || |||||||| || ||||| |||||||| || || ||||| || | |
-------------------------------gcaagtgttttttc--gctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 8
ttcaagtgttagattacaat-ccttacaaaatgtctgtgttatttccaacacctg-tagcttacatgtttaaagctta-------attgcttattttttttctctct--agTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
||| || ||| | || || || | | || | || | | ||| |||| ||| || | | ||| || || | | | ||||||| |||||||| || ||||| || || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || || | ||||||
-gttagtaatatatttctatatatttcactggaccaattttttaattaatttgaggcaatttagttgttaaaaactgattgtgccactgccacttgcattaccttttacagTTTCTGAAGTTTGTTGAAAAGACTGCCCCTATTGCTGTTTATACTTCTGGAAAAGGCTCATCAGCGGCTGGCCTGACCGCTTCTGTAATCCAAGATAGTG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------ttcaagtgttagattacaatccttacaaaat-gtctgtgttatttccaacac-ctgtagcttacatgtttaaagcttaattgcttattttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
|| | ||||| | | || || | | || |||| ||| |||||||| | | | | ||| ||| ||| | | ||||||| |||||||| || ||||| || || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || || | |||||||
gttagttttatgtgtatatatattttgccagaccaattttttaattaatttgtggcaattgagttgttaaaaacctattgggccactgccattttcattttttcgttcacattgtagcttgttttctcctg--tgagttgaccattaccttttttac-agTTTCTGAAGTTTGTTGAAAAGACTGCCCCTATTGCTGTTTATACTTCTGGAAAAGGCTCATCAGCAGCTGGCCTAACCGCTTCTGTAATCCAAGATAGCG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 8
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgcttattt-----tttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
| | ||| | || | | ||||| | | | | || | ||| | | | | ||| || || || | || || | ||| ||||| | |||||||| |||||||| |||||| | |||||||||||||| || || || ||||| |||||||| || |||||||||||||||||||||| |
----acttggagaaaagaaactcaaaaaaatttaaatttaagatcttgctcctctttcattgttacataa-gcctaggcactgacttgatgattactttctgaagTTTTTGAAGTTTGTTGAGAAGACTGCTCCAGTAGCTGTTTATACATCAGGGAAAGGCTCATCAGCTGCTGGTCTTACAGCTTCGGTGATTCGAGATAATA
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 9
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgcttatttttttt-ctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
| ||| || | ||| | ||| | ||||| | | | ||| | || |||| || || | |||| || || ||||| |||||||| || || |||||||||||||| ||||||||||| || || ||||||||||| || || || || ||||| || |
-tttagttcccttcagtaaagttctgggtccgtcgactgggatggcaatagctgtacataatacccacgaaggatgtgtgtgtattgccttggctatgcagTTCCTAAAATTTGTTGAGAAGACTGCACCGATTGCTGTTTATACCTCTGGAAAGGGCTCCTCAGCTGCTGGGCTTACTGCATCCGTTATTCGTGACTCTA
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ17142 (Selaginella moellendorffii), 3'ss of exon 9
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgcttattttttttctc-tctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
|| | | | ||| ||| || || | |||| || | ||||| | || ||||||||||| || || || |||||||| ||||||||||| |||||||| || |||||||| | || || || || || || ||| |
--------------------------------------------------gttggatttcagtgctttggttcttgtttctctaatgttttccttgtacagTTTTTGAAATTTGTGGAGAAAACTGCGCCGATTGCTGTGTATACATCTGGCAAGGGTTCCTCTGCTGCTGGATTGACTGCATCCGTCATACGTGATGCGA
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ31205 (Selaginella moellendorffii), 3'ss of exon 9
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgctt--attttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
| || || || | | || || || |||| | | ||||| | || ||||||||||| || || || |||||||| ||||||||||| |||||||| || |||||||| | || || || || || || ||| |
---------------------------------------------------gttggatttgagtgctttgggtcttgtttctctaatgttttccttgtacagTTTTTGAAATTTGTGGAGAAAACTGCGCCGATTGCTGTGTATACATCTGGCAAGGGTTCCTCTGCTGCTGGATTGACTGCATCCGTCATACGTGATGCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacacctgtagcttacatgtttaaagcttaattgcttattttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
ttgcttattttttttc CT-rich tract
tttaaagcttaattgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgcttattttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - -tacaaaa
- - - - - - - - - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttaaagc