Sequence
atgc intronic sequence ATGC exonic sequencegtatatcagtttaattgaatattatgtctgttactggtttatttggttacaggatatgtttatggaagtgcctcttacctgtccactgaaatttgcagGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28470.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 12
----gtatatcagtttaattgaatatta-tgtctgttactggtttatttggttacaggatatgtttatggaagtgcctcttacctgtccactgaaatttgcagGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
| | ||||| | | || | | ||| | || | || | ||| | || | | || || | | || | | |||| |||||||||||||| ||||||| ||||| ||||||| ||||||||||| || || || |||| |||||||| |||||||||||||||||||| |
tcagaaaaaaaagtttcttgatgtgctactttttgtctcaagtgtgccactttgttgattat--ctgtgaaccttatgtttcactctgc-ttgttactcctagGCACACTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
gtatatcagtttaattgaatattatgtctgttactggtttatttggttacagga-tatgtttat-ggaagtgcctcttacctgtc-cactgaaatttgc----agGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
|||| || | || | || |||| || | | | | |||| || | ||| |||| | || | ||| || | |||| || ||||||||||| ||||||| ||||| ||||||| || |||||||| || || || |||| |||||||| |||||||||||||||||||| |
-----tcagaaaaaaaagtttatagatgtgctactttttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT
upper sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
gtatatcagtttaattgaatattatgtctgttactggtttatttggttacaggatatgtttatgga--agtgc----ctcttacctgtccact-gaaatttgc-agGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
| || | | | ||| |||| || | | | ||||| ||| || |||| | || |||| ||| ||| | | || | | ||||| |||| || ||||||||||| ||||||| ||||| ||||||| ||||| || || || || || | || |||||||| |||||||||||||||||||| |
--acatgaaa--gactcaattttataggtgcttcag--ttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttacaggatatgtttatggaagtgcctcttacctgtccactgaaatttgcagGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
ctcttac putative branch site (score: 3)
atatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatcagtttaattgaatattatgtctgttactggtttatttggttacaggatatgtttatggaagtgcctcttacctgtccactgaaatttgcagGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA