Sequence
atgc intronic sequence ATGC exonic sequence...gtgcctgttagagataaataatggaactttaaactatatctttgtcaccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G17440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 3'ss of exon 9
gtgcctgttagagataaataatgga--actttaaactatatctttgtcaccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
| || | ||| |||| | | || || | | | | | |||| ||| || || | | | | | || | | | ||||| || || || || ||||||||||||||||| ||||| ||||||| |||||||| || || || || | || || |||
-tatcttgttaagaattctaataaattatcacaatcttttacataatagcatgcgtgttgtttacaattaata-tcttagcttacaattttcttccaaacagTGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 9
gtgcctgttagagataaataatggaactttaaactatatctttgtcaccaatctgttatttgcatttggca-atgtcaaaaatctg--ttgtactgccttta--gTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
|||||| || | | || | |||||| | | | ||| | || | || | || | | || ||||| | ||| ||||||| || |||||||||||||||||||| || ||||| || || || |||| ||| || || || || || || |||||
----tagttagaaatttttggggaaataatgccatatatcaatat-attgtcctgctgcttttgtatgttttgctttaatattttgatttgtattattattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
gtgcctgttagagataaataatggaact-ttaaactatatctttgtcaccaatctgttatttgcatttggcaatgtcaaaa-----atctgttgtact--------gcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
||| |||| |||| || | ||||||| | | | |||||| | | ||||| || |||| | ||||| | || | || ||||| ||||| ||||| |||||||||||||| |||||||| ||||| || |||| ||||| || || ||||||||||||||
-----------aga-aaattatggggctaccatactatatgtggat--tctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
----gtgcctgttagagataaataatggaactttaaactatatct-ttgtcaccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
|| || | | | ||| | || | | | ||| |||| || || ||| | | | | || | || | | || ||||| ||||| | || || ||||||||||||||||| || ||||||||||||| ||| || || || | | || | |
ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttt----tttgct-taatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ22509 (Selaginella moellendorffii), 3'ss of exon 9
gtgcctgttagagataaataatggaactttaaactatatctttgtcaccaatctgttatttgcatttggcaat---gtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG------------------
|||| |||| || ||| | | ||||||| || | | | |||||||| ||| | |||||||||||||| || ||||||||| | || ||||||| |||||||| || | | || |||| |
-------------------------------------------------gtactgtagtttg-atgtggtattcttgtcaaaatctcatttcatgtcatgcagTGATCGACGGCTCGCTGATCATTTTGGTGGAAAGCTTCACCTCGGATACATGCGCATCCGCGAAAAGCTCGGCGAACTTCGGGTAATCTTCCGGATGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
ctgccttt CT-rich tract
tgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcctgttagagataaataatggaactttaaactatatctttgtcaccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - -agataaa
- - - - - - - - - - - - - - - aaactat
- - - - - - - - - - - - - - - - - - - - - - -caccaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaat