Sequence
atgc intronic sequence ATGC exonic sequence...acatatccatcatgattccctttatgtctttcctttactgtattttcttttatcttcatcaattatgatcttattgtatctgatacctttaaatttgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
Basic information
species | Glycine max |
transcript | GLYMA20G35110.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------------------acatatccatcatgattccctttatgtctttcctttactgtattttctttta--------tcttcatcaat-tatg---atcttattgtatctgatacctttaaatttgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
| | || | | | ||| || || |||| | | |||| || |||| ||| |||| |||| || || || || |||||||||||||||||| ||||||||||||||| || || || |||| | || ||||||| |||||||| ||| ||||||| |||| || || || || |
gtaccaatcctcactttttgtggactttaactctgttctagacttctagtaatctcaaatttttgcattcgatttagttcttgatcttctaatgatacctctttggtaatatatgcacatctctgaatacttgttattgtttttaatgcagATAGTAAATTGGAAAAATTATTTAAAATTCCCTGATGAGGTTAGGCTATCACCAGAAGCCAAGGATCTAATTTGTAGACTTTTATGCAACGTAGAACAAA
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------acatatccatcatgattcc--ctttatgtctttcctttact----gtattttcttttatcttcatcaattatgat-------cttattgtatctgatacctttaaatt--------tgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
| || || | | || | ||||| | |||| | || |||| | | |||| |||| | || |||| ||| | ||| || ||||||||||||||||||||||||| || ||||| ||||| || |||| | | || ||||||| |||||||||||| |||| || |||| ||||| || || |
gtaattaatccattcctttttgaatctttcattttaatattgaaggcagactggcgatttcaagtcttacatttaattttagtctttttgtatctctttggtaattctaatgtggaaacttacctcttctcgattcattatcttcccccttatgcagATAGTAAATTGGAGAAATTACTTGAAATTCCCAGATGAGGTTAGACTATCACCAGAAGCCAAGGATCTTATTTGTAGGCTTTTATGCAATGTTGAACAAA
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 7
acatatccatcatgattccctttatgtctttcctttactgtattttcttttatcttcatcaattatgatcttattgtatc-----tgatacctttaaatt-tgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
||| || ||| | | || || ||| | | ||| || |||| | || | | | || || || || | | | || || |||||||||| ||||||| | || |||||||||||||||||| || | || ||||||||||||| |||||||||| ||| |||||||||| || ||||
------gcattattattttttcattttccttatttttttaattcttccctttccttccttttttttcctttccgtgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttatcttcatcaattatgatcttattgtatctgatacctttaaatttgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
atctgat putative branch site (score: 4)
aattatgatcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatatccatcatgattccctttatgtctttcctttactgtattttcttttatcttcatcaattatgatcttattgtatctgatacctttaaatttgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG