Sequence
atgc intronic sequence ATGC exonic sequenceATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccc--tttttttgctttttggctg---tcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa
||| ||||| | ||| || || ||||||||||||||| | ||||||||||||||||| ||||| ||||| || ||||||||||| | |||||||||||||| |||| || || | |||| | || | |||| | || || || | ||| ||| | | ||| ||
ATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCACAACACTTCATCCGTTTAGTACAAAGAAGgta-tgtcaggctcttaattgaataactttacagttggtttggtttcaatctgctctaatgtaacttcagtaaata-atttccaccacaaaagctgataggg---
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgt--aacatcagct--tccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa
| | ||||| ||||| || || |||||||| |||||| | |||||||||||||| || ||||| || |||||||| |||||||| || || |||||||||| | | ||| | || |||| | | |||||| | | | | || | || | || | | | | || || | ||||
ACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTCAGCATTTCATCCGTCTAGTGCAAAGAAGgttgatttttggctagttttcccccttcaattttagttatcattt-gtctccaatagt--tagttaacatttctccctgttcaatttctatacttactttttg-
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaa--catcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcata--ctcaaaacttat--agattattatcttaaatttccatcttttaa
| ||||| || || || || |||||||| ||||| | ||||||||||| ||||| ||||| || || || || ||||||||| | ||||||||||||| | |||||| || | | |||| | | | | | || | | ||||| | | || ||||| | | | | | || |||||| | |
AGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCCAACATTTCATCCGCTTAGTACAAAGAAGgtcagtcatcaggtttctgtaatttg-tctctagttacagttc--atttgcgttgttgtgtgcttgtaacttgacaaaaaaagtgttatatgcttccatttgt---
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA09G00430.2 (Glycine max), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatct-taaatttccatcttttaa
| || || ||||||||| | ||||| ||||| |||||| | ||||||||||||||||| ||||| |||||||| |||||||| ||| | ||||||||||||||| | || | || | | | | | | || || | | | | | | |||| || ||| | ||||| | ||||
AAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTCAACACTTCATTCGCTTGGTACAAAGAAGgtaatttggactaatttcttgaatggatctagatcccctctcattgggtgatctgttccctactctttattatttgttagcaactaattttttttttttg-
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattat-tatct-taaatttccatcttttaa
| || || ||||||||| | ||||| ||||| |||||| ||||||||||||||||||| ||||| |||||||| |||||||| ||| | |||||||| |||||| | | | | || | | | | | || ||| || ||| | || ||| | || | ||| | | | | | ||||
AAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTCAACACTTCATTCGCTTGGTACAAAGGAGgtaatttggacatatttcttgaatggatctagatcctctctcatttggggtgatc-tgttccctactctttatttgtctatttgttagcaactactttttt-
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagctt----ccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa
| | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| ||||| || ||||| || || | ||||| || |||| ||| | | ||| || |||||| | | | | ||| | || || | | |||| || || | ||
AGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCACAACACTTTATTCGTTTAGTACAGAGGCGgtatgttcaatatatgacacttgttacactttttttatttatgaattaataatcttaatgtccttaatgggtgcattaatttatttttcatgtgggactc----
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagctt----ccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa
| | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| || || || ||||| || || | || || || |||| ||| | | ||| || |||||| | | || || | | ||| || | | | |||| ||| ||| ||| | |
AGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCCAACACTTTATTCGTTTAGTGCAGAGGCGgtatgttcaatatatgacacttgttacactttttatttat--ttatgaatta-ataatcttaatgtccttattgggtgcattaatttat-ttttcatacgtgag
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa----
| || || |||||||| || ||||| ||||| |||||| | ||||||||||||||||||||||| || |||||||| |||||||| || || ||||| |||| | | || || || | ||| | |||| | ||| || | || | || ||| || || ||
AAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTCAGCATTTCATCCGTCTGGTGCAAAGGCGgta-tgctaaatgttaaattgatgagagatgatttatattatatctt---ttataaatttcattgagagtaaaaaatctgcaaaattttacacctattgtgttt
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcat--actcaaaacttatagattattatcttaa--atttccatcttttaa-------
||| |||||||||||||||||||| ||||| ||||| |||| ||||||||||| || ||||| || ||||| |||||||| || | || ||||||||||| | | || | | | || | ||| | | | || ||| | | |||||| | |||||| | | |||| | | |
ATGTGTTCAAGAATGAAGCTAAGAAAATGGTGGTTGCCCTAGTGGATATGGAGCGAGCTTTTGTGCCCCCTCAACACTTCATTCGTTTGGTGCAAAGAAGgtactgggaa----------tatgatataagcctatatttttggatc-cattgtcaataagtagaaacttttgagctattattgttactgtttcagtaaactcaaaaaaaa
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 5'ss of exon 12
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatag--attattatcttaaatttcc----atcttttaa-------------------------------------
||| | | ||||| ||||| ||||| ||||| | ||||||||||||||||||||| | || ||||| ||||| ||| | || || || | ||||| | | | |||| | || | | || | | | | | | | | ||| | || | | || | ||| ||| || ||
ATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTCAACACTTTATCAGACTTGTTCAGCGCAGgtagagcttggcttgatatttt-gtcttgtagttggggatcagtgcagaggaaacctcctctgatctatttgcggctactggtttatgtttagcgaggtcgttcgggtgtttatttttctgataaagtgttacacttaaacagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164231051|gb|ES022297.1|ES022297EST: CCGCCTCGTACAAAGAAG AATGGAAAGGCAGCGTCGTGAGGAGGAGCTGAAAGGTCGTTCCTCTAAAAA
genomic: CCGCCTCGTACAAAGAAGgtaacatcag ... tctttatcagAATGGAAAGGCAGCGTCGTGAGGAGGAGCTAAAAGGTCGTTCCTCTAAAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTCAGCACTTCATCCGCCTCGTACAAAGAAGgtaacatcagcttccctttttttgctttttggctgtcatttcgagtggcgttatcatactcaaaacttatagattattatcttaaatttccatcttttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcaaaa