Sequence
atgc intronic sequence ATGC exonic sequence...ttcgatgaatttgtatgtaacaattaagtattttgtggtataaggattaatgataatattattgtatttgatagtcttacccttcgaataatttttgcagGGAAACGGTCTCCTTCGGGCACTTTATGTTGCTGCCTTTGCAGTTTCCGGATATGCGTCATCTGAAGGTCGTAATTGTAAACCCTTTAATCCTTTATTAG
Basic information
species | Glycine max |
transcript | GLYMA01G41940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 5
ttcgatgaatttgtatgtaacaattaagtat-tttgtggtataaggattaatgataatattattgtatttgatagtc-ttacccttcgaataatttttgcagGGAAACGGTCTCCTTCGGGCACTTTATGTTGCTGCCTTTGCAGTTTCCGGATATGCGTCATCTGAAGGTCGTAATTGTAAACCCTTTAATCCTTTATTAG
| | || | | ||| | |||| | ||| | | | || | || | || | |||| || || ||| | | ||| |||||||| ||||||| | | || ||||||| || ||||| ||||| ||||||||||| ||||||||||| |||| |||||||| || || || |||
aatgctaaaatattttgtgattgttaaagacgtttactgctttaacatct-tcatgaaatc-tgacatttttccctcattgggctttcctttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGCTAG
upper sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 3
ttcgatgaatttgtatgtaacaattaagtat-tttgtggtataaggattaatgataatattattgtatttgatagtc-ttacccttcgaataatttttgcagGGAAACGGTCTCCTTCGGGCACTTTATGTTGCTGCCTTTGCAGTTTCCGGATATGCGTCATCTGAAGGTCGTAATTGTAAACCCTTTAATCCTTTATTAG
| | || | | ||| | |||| | ||| | | | || | || | || | |||| || || ||| | | ||| |||||||| ||||||| | | || ||||||| || ||||| ||||| ||||||||||| ||||||||||| |||| |||||||| || || || ||||
aatgctaaaatattttgtgattgttaaagacgtttactgctttaacatct-tcatgaaatc-tgacatttttccctcattgggctttcctttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaatgataatattattgtatttgatagtcttacccttcgaataatttttgcagGGAAACGGTCTCCTTCGGGCACTTTATGTTGCTGCCTTTGCAGTTTCCGGATATGCGTCATCTGAAGGTCGTAATTGTAAACCCTTTAATCCTTTATTAG
gtcttac putative branch site (score: 3)
tttttgc putative PPT
ataatattattgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcgatgaatttgtatgtaacaattaagtattttgtggtataaggattaatgataatattattgtatttgatagtcttacccttcgaataatttttgcagGGAAACGGTCTCCTTCGGGCACTTTATGTTGCTGCCTTTGCAGTTTCCGGATATGCGTCATCTGAAGGTCGTAATTGTAAACCCTTTAATCCTTTATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - -tgtatgt
- - - - - - - - - - - - - - - ttttgtg