Sequence
atgc intronic sequence ATGC exonic sequence...caatgtaaaaatacttcaaacttcaatactatatagttagcttaggggtgaaaagtttaagtagtttgtattaatagtcttctttttactttccttgcagTCTACTATGCCTTCAAGCGAGAAGCATCCATCACACGTGCCAATGTGGAAAGGGGTCAAGGTTTCTTACACGATCATTGCAGCATGCTTATTTCCCATGG
Basic information
species | Glycine max |
transcript | GLYMA01G36590.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36590.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0302g00020.t01 (Vitis vinifera), 3'ss of exon 3
caatgtaaaaatacttcaaacttcaatactatatagttagcttaggggtgaaa-agtttaagtagtttgtattaatagtcttctttttact--ttccttgcagTCTACTATGCCTTCAAGCGAGAAGCATCCATCACACGTGCCAATGTGGAAAGGGGTCAAGGTTTCTTACACGATCATTGCAGCATGCTTATTTCCCATGG
| | || | | ||| || || | || | | | | |||||| || ||| | ||||| ||| | | |||||| | || |||||||| ||||||||||| ||||| | |||||| ||||||||||| || ||| |||| ||||| |||||||| ||||||||||| | |
ccccttcaacacgttccaatttttaaagcaattctgcagacctcttccccccacagtttacgt---ttgctcaggatcttttcttgttaataatatgttgcagGCCACGATGCCTTCCAGCGAGAAGCACCCATCTCGCGTGCCCATGTGGAAAGGAGTAAAGTTTTCATACACCATCATTGCTTTGGGCTTATTTCCCCTTG
upper sequence: GLYMA01G36590.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g03530.t01 (Vitis vinifera), 3'ss of exon 3
--caatgtaaaaatacttcaaacttcaatactatatagttagcttaggggtgaaaagtt-taagtagtttgtattaatagtcttctttttactttccttgcagTCTACTATGCCTTCAAGCGAGAAGCATCCATCACACGTGCCAATGTGGAAAGGGGTCAAGGTTTCTTACACGATCATTGCAGCATGCTTATTTCCCATGG
| | |||||| | | | | || | | |||| |||| ||| || | | | || || | ||| |||| |||||| | || ||||| || ||||||||||||||||| |||||||||||||| || ||||||||||| || ||||| |||||| || | | |||| |
atagacttttggttacttcgtatgtttgatttggttgaata--tatgctttgaatagttgtaattaaatatgggtttttgttttttgtttgctttt-ttgcagGCCACAATGCCATCTGATGAGAAGCATCCATCACATGTGCCAATGTGGAAGGGTGTCAAGGTTTCATATACGATAATTGCATTGTGTCTCTATCCCCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggtgaaaagtttaagtagtttgtattaatagtcttctttttactttccttgcagTCTACTATGCCTTCAAGCGAGAAGCATCCATCACACGTGCCAATGTGGAAAGGGGTCAAGGTTTCTTACACGATCATTGCAGCATGCTTATTTCCCATGG
tattaat putative branch site (score: 2)
tcttctttttactttc putative PPT
tttaagtagtttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgtaaaaatacttcaaacttcaatactatatagttagcttaggggtgaaaagtttaagtagtttgtattaatagtcttctttttactttccttgcagTCTACTATGCCTTCAAGCGAGAAGCATCCATCACACGTGCCAATGTGGAAAGGGGTCAAGGTTTCTTACACGATCATTGCAGCATGCTTATTTCCCATGG
- - - aaaaata
- - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - -aggggtg