Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtgtcaaatttcttattttatagatatgagatgtcatgcattttcttaacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
Basic information
species | Glycine max |
transcript | GLYMA11G05490.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G05490.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090715_T01 (Zea mays), 3'ss of exon 3
gtgtgtgtcaaatttcttattttatagatatgagatgtcatgcattttcttaacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
|| | ||| |||||| ||| | ||| || | || ||||| | | || ||| |||| ||| ||| |||| |||||||||||||||| ||||| || ||||| ||||||||||| || ||| ||||| || | ||| | | ||||| | || ||||| ||||| ||||||
gtat-tgtataatttcctatatgata---atcgatccttat-tatttttgtggtacatattttt-attag---------------ctaactttaaactggcaacagTCCATATTACAACATTGAGTTAAAGGAAATACATGTTGCTGGAAAGGCACTGCGGGTAGATTCAAGGATCTTTGACAGCAAGCATGGGACTGTTTTGGAT
upper sequence: GLYMA11G05490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgtgtgtc-----aaatttcttatttt-atagatatgagatgtcatgcattttcttaacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
|| ||| || ||| ||| || | || | | | || || || || |||||||| | ||| || | |||||||||||||||||||| |||||||||||||||||||||||||||| ||||||| || ||||| |||||| ||||||| || | | | | | || ||||| ||| ||||||| | || | ||
gtatgtttccaagggaatggctttttctgattggtgaatgggatcttgtataatcctaacaaatacgtttaatacctttcacacatttactctagtttcgggatggcgacagTCCATATTACAATATAGATTTGACGGGGATACGTGTTGCTGGGAAGCAGTTGTCTCTTCATTCGAGAGTCTTTGACGGGGAACATGGCGCCGTACTAGAC
upper sequence: GLYMA11G05490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0129g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtgtg-tgtcaaatttcttattttatagatatgagatgtcatgcattttcttaacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
|| || | | |||| | |||| || ||||||| | | | || | ||| || ||||||| || | ||||||||||||||| | ||||||| ||||| |||||||||||||||| ||||||||||||| |||| ||||||| ||| | ||||||||| |||||||||||| ||| |||| || || |||||
gtttggtttgaaatattttatcttgtagatataaaacactacattcttccctaatgtataaatttgatacatatggcacatttactctagtctcgggatgggaacagTGCATATTACAATATTGACCTGAAGGAGATACACATTGCTGGGAAGCAGTTGCCTATAAACCCAATGGTTTTTGATGGAAAATATGGGACAATCCTGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
atttgattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtgtcaaatttcttattttatagatatgagatgtcatgcattttcttaacaaatgcatttgattaatctcacacatttactctagttttgggatggcgacagTCCATATTACAATATTGATTTGAAGGAGATACATGTTGCGGGGAAGCGACTGCATTTAAACCCAAAGGTTTTTGATGGGAAACATGGAACTGTCTTGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA