Sequence
atgc intronic sequence ATGC exonic sequence...tttaattattttttatttagcctcctatagttcagttgaaagatgacattgtttaatgctattgaatgtggcagttcaaacctttgagttttattttcagGGAAACAGTCTCCTTCGGGCACTGAATGTTGCTGCCTTTGCAATTTCTGGATATGCATCATCTGAAGGTCGTCATTGTAAACCCTTTAATCCATTGTTAG
Basic information
species | Glycine max |
transcript | GLYMA05G04340.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 5
----tttaattattttttatttagcctcctatagttcagttgaaagatgacattgtttaatgctattgaatgtggcagttcaaacctttgagttttattttcagGGAAACAGTCTCCTTCGGGCACTGAATGTTGCTGCCTTTGCAATTTCTGGATATGCATCATCTGAAGGTCGTCATTGTAAACCCTTTAATCCATTGTTAG
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aatgctaaaatattttgtgattg---ttaaagacgtttactgctttaacatcttcatgaaatctgacatttttccctcattgggctttcct-ttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGCTAG
upper sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 3
----tttaattattttttatttagcctcctatagttcagttgaaagatgacattgtttaatgctattgaatgtggcagttcaaacctttgagttttattttcagGGAAACAGTCTCCTTCGGGCACTGAATGTTGCTGCCTTTGCAATTTCTGGATATGCATCATCTGAAGGTCGTCATTGTAAACCCTTTAATCCATTGTTAG
| || |||||| | || | | | | || | | || | || || | | | | | || |||| ||| |||||||||||||||| | | || ||||||| || ||||| ||||||||||||| || ||||||||||| ||||| |||||||| || ||||||||||
aatgctaaaatattttgtgattg---ttaaagacgtttactgctttaacatcttcatgaaatctgacatttttccctcattgggctttcct-ttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattgtttaatgctattgaatgtggcagttcaaacctttgagttttattttcagGGAAACAGTCTCCTTCGGGCACTGAATGTTGCTGCCTTTGCAATTTCTGGATATGCATCATCTGAAGGTCGTCATTGTAAACCCTTTAATCCATTGTTAG
gtttaat putative branch site (score: 4)
ttttattttc putative PPT
tttgagttttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaattattttttatttagcctcctatagttcagttgaaagatgacattgtttaatgctattgaatgtggcagttcaaacctttgagttttattttcagGGAAACAGTCTCCTTCGGGCACTGAATGTTGCTGCCTTTGCAATTTCTGGATATGCATCATCTGAAGGTCGTCATTGTAAACCCTTTAATCCATTGTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG