Sequence
atgc intronic sequence ATGC exonic sequencegtgattacacagagatatgcactgttaagtgttttcgatctacgtggcatttctgaaataacttcatggtcaaatatatatagGTTAATGGTTTTGTAGAAGATGTAACTGGAAAAAAGGCTGCGACGGTATTTGGTAAATGGAATGATAGCCTTTATTATGTTGCTGGTGATGGAATCAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12460.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 8
---------------------gtgattacacagagatatgcactgttaagtgttttcgatctacgtggcatttctgaaataacttcatggtcaaatatatatagGTTAATGGTTTTGTAGAAGATGTAACTGGAAAAAAGGCTGCGACGGTATTTGGTAAATGGAATGATAGCCTTTATTATGTTGCTGGTGATGGAATCAACA
|| | | || || | || | ||||||| | |||| ||| | || | || | | || ||||| |||| ||||| ||||||||||| |||||||||| ||| || ||||||| || ||| |||| ||| ||||||||||| ||| || | | |
cccgcacgtggtcccactcaaaatatcaga-aggaatcttatcttctttgtgttttttacctaccaaattgttcactag-aatgtgctg--tatgtctaattagGTGCATGGCTTTGTTGAAGATGTAACGGGAAAAAAGGTTGCCACATTATTTGGCAAGTGGGATGACAGCATTTATTATGTTAATGGCGAAGTGAATGTGA
upper sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 8
--------------------gtgattacacagagatatgcactgttaagtgttttcgatctacgtggcatttctgaaataacttcatggtcaaatatatatagGTTAATGGTTTTGTAGAAGATGTAACTGGAAAAAAGGCTGCGACGGTATTTGGTAAATGGAATGATAGCCTTTATTATGTTGCTGGTGATGGAATCAACA
| || || || | || ||||||| | ||| ||| | || | || | | || ||||| |||| ||||| |||||||||| |||||||||| ||| || ||||||| || ||| |||| ||| ||||||||||| ||| || | | |
tgcccgcacgtggtcccactcaaaatatctgaaggaatcttatcttctgtgttttttacataccaaattgttcattag-aatgtgctg--tatgtctaattagGTACATGGCTTTGTTGAAGATGTAATGGGAAAAAAGGTTGCCACATTATTTGGCAAGTGGGATGACAGCATTTATTATGTTAATGGCGAAGTTAATGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttttcgatctacgtggcatttctgaaataacttcatggtcaaatatatatagGTTAATGGTTTTGTAGAAGATGTAACTGGAAAAAAGGCTGCGACGGTATTTGGTAAATGGAATGATAGCCTTTATTATGTTGCTGGTGATGGAATCAACA
aaataac putative branch site (score: 2)
tcaaatatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattacacagagatatgcactgttaagtgttttcgatctacgtggcatttctgaaataacttcatggtcaaatatatatagGTTAATGGTTTTGTAGAAGATGTAACTGGAAAAAAGGCTGCGACGGTATTTGGTAAATGGAATGATAGCCTTTATTATGTTGCTGGTGATGGAATCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA