Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtttcaaaacttttatcttctagatatgagatgtaatgcattttcttaacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
Basic information
species | Glycine max |
transcript | GLYMA17G17990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090715_T01 (Zea mays), 3'ss of exon 3
gtgtgtttcaaaacttttatcttctagatatgagatgtaatgcattttcttaacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
|| || | || || || |||| ||| ||||| | | || |||||||| ||| || |||| |||||||||||||||| ||||| || ||||| ||||| |||||||| ||| ||||| || | ||| | ||||| | || ||||||||||| ||||||
--gtattgtataatttc---ctatatgataatcgatccttattatttttgtggtacatat-ttttattag---------------ctaactttaaactggcaacagTCCATATTACAACATTGAGTTAAAGGAAATACATGTTGCTGGAAAGGCACTGCGGGTAGATTCAAGGATCTTTGACAGCAAGCATGGGACTGTTTTGGAT
upper sequence: GLYMA17G17990.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgtgtttcaaaac------ttttatcttctagatatgagatgtaatgcattttcttaacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
|| |||||| || ||| ||| | | | | | || || || |||||||| | ||| || | |||||||||||||||||||||||| |||||||||||||||||||||||| ||||||| || ||||| ||||||||||||| || |||| | | | || ||||| || ||||||| | || | ||
gtatgtttccaagggaatggctttttctgattggtgaatgggatcttgtataatcctaacaaatacgtttaatacctttcacacatttactctagtttcgggatggcgacagTCCATATTACAATATAGATTTGACGGGGATACGTGTTGCTGGGAAGCAGTTGTCTCTTCATTCGAGAGTCTTTGACGGGGAACATGGCGCCGTACTAGAC
upper sequence: GLYMA17G17990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0129g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtttcaaaac-ttttatcttctagatatgagatgtaatgcattttcttaacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
|| || || ||| ||||||||| ||||||| | | | || | ||| || |||| || || | ||||||||||||||| ||||| ||| ||||| |||||||||||||||| |||||||||||||| |||||||||||| ||||| ||||| ||| ||||||||||||||| ||||||| || |||||
gtttggtttgaaatattttatcttgtagatataaaacactacattcttccctaatgtataaatttgatacatatggcacatttactctagtctcgggatgggaacagTGCATATTACAATATTGACCTGAAGGAGATACACATTGCTGGGAAGCAGTTGCCTATAAACCCAATGGTTTTTGATGGAAAATATGGGACAATCCTGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
atgcattttattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtttcaaaacttttatcttctagatatgagatgtaatgcattttcttaacaaatgcattttattaatctcacacatttactctagtttcggggtggcgacagTCCATATTACAATATTGATTTGAAGGAGATACACGTTGCTGGGAAGCGACTGCCTCTAAACGCAAATGTTTTTGATGGAAAACATGGGACTGTCTTGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA