Sequence
atgc intronic sequence ATGC exonic sequencegtattttcctttttaactttcctcattacatcaatgcttctgcttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15660.1 (Oryza sativa), 3'ss of exon 4
gtattttcctttttaactttcctcattacatcaatgc-------ttctg-----cttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA
| ||| | |||||| | || | | ||| ||| || | ||| ||||| ||| || | | | || ||||||||||||| |||||||||||||| ||||| |||| |
caacttttcaggttaactgaacgtatcataaatgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaattattattatcatt--tttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGA
upper sequence: AT1G19690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15660.2 (Oryza sativa), 3'ss of exon 1
gtattttcctttttaactttcctcattacatcaatgc-------ttctg-----cttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA------------------------------------------------------------
| ||| | |||||| | || | | ||| ||| || | ||| ||||| ||| || | | | || ||||||||||||| |||||||||||||| ||||| |||| |
caacttttcaggttaactgaacgtatcataaatgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaattattattatcatt--tttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
upper sequence: AT1G19690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119749_T04 (Zea mays), 3'ss of exon 4
---------gtattttcctttttaactttcctcattacatca-atgcttctgcttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA------------------------------------------------------------
||| | | | || | || | || || || |||| || | || || | | |||| | ||||||||||||||||| ||||||||||||| | ||| |||| |
gagtcgagggtaataacaaatcatgctatgtgcagtgcaccatataagagattttccttagaaaactactctgtaacgctttacgctttcttacttgcagGTGTGTATGGTGATTGTGGTGGTGTATTGGTTGATGAGGAGTAAGGGACTCGTTGGTTCTTTTCTCGTCCATGAAGTACATTTTAATAGAAAGCTAAATA
upper sequence: AT1G19690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119749_T02 (Zea mays), 3'ss of exon 4
---------gtattttcctttttaactttcctcattacatca-atgcttctgcttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA
||| | | | || | || | || || || |||| || | || || | | |||| | ||||||||||||||||| ||||||||||||| | ||| |||| |
gagtcgagggtaataacaaatcatgctatgtgcagtgcaccatataagagattttccttagaaaactactctgtaacgctttacgctttcttacttgcagGTGTGTATGGTGATTGTGGTGGTGTATTGGTTGATGAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttctgcttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA
ttacaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttcctttttaactttcctcattacatcaatgcttctgcttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG