Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatgatgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
Basic information
species | Glycine max |
transcript | GLYMA18G46440.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 5
gtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatgatgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
| ||| | || ||||| | ||| || | | ||| | || | |||| | | || || || ||| | || || | ||||||||||| ||||||||||| || | ||||| || || |||||||||||||| |||||||| |||||| | || || ||
------actgagtttgagatgctccttgacctgctagtta-------gagatctttattttcctaattaagtataattatgaacatgat--caaattaatcttatctatgg------------gcagGCAAATGTCTATCATGCAACAAAGACGGATGGCCAGGAGCTTGCAATTAAAGTCTACAAAACCTCTGTTCTTGTTTTTAA
upper sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 3
gtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatgatgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
||| | ||| | || ||||| | ||| || | | ||| | || | |||| | | || | || ||| | || || || ||||||||||| ||||||||||| || | ||||| || || |||||||||||||| |||||||| ||||| | || || ||
-----tgagtc-tttgagatgctccttgacctgctagtta-------gagatctttattttcctaattaagtataattatgaacatggt--caaatt---aatcctatctatg---------ggcagGCAAATGTCTATCATGCAACAAAGACGGATGGCCAGGAGCTTGCAATTAAAGTCTACAAAACCTCTGTCCTTGTTTTTAA
upper sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatgatgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
| | | || || | | | | ||||| | ||| | || | | ||| | | || || || | | || | || || | | ||||| |||||||||||||| || |||||||| ||| ||||||||||| ||||| ||||| ||||||||| |||| || ||
---------------gtatgtcacattcac-tactctcatatttgatggtttagctatttag----tcaagaagatgatctgtttggattcctttgttgaaagtact-ctcttttattgtttttcagGCTAATGTTTATCATGCCACAAAATCTGACGGTTCGGAACTTGCAATAAAAGTGTACAAGACATCTGTTCTGGTTTTTAA
upper sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatg-atgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtg-ttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
|||||| || || | || | || ||| || | | | || || || | || || ||| |||||||||||||||||||| || |||||||| ||| ||||||||||| ||||| ||||| ||||||||| |||| |||||
----------------------------------------gtatgatacatttcacaactctcatatttgagattatctgtttttattcttttttgttgaaagcactctctttaattattgtctttcagGCAAATGTTTATCATGCCACAAAATCTGACGGTTCGGAACTTGCAATAAAAGTGTACAAGACATCTGTTCTGGTTTTCAA
upper sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtatgtgatccacc-tga-agcttttgtttacctgtttgttt---ttatgatgatgacatggtttggatcatcg-actatatgtgat-atcaagacaccacatt-tctgtttc-----ttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
| | | ||| | ||| |||| | | ||| | || || || ||||| | | || || || | | | | ||| | |||| | | || || | ||||| ||| ||| | |||| ||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||| |||||||| |||||| | ||||| ||
gtacgtggatccttacatccttcaatttattatctattatgatagctatagcctaca-gcatgcttcaattttgatgtttatgaagtctgcatttgtgtattttctgtcctgatcatgtgatcattttctttgttttcattattattgttattttttttaacagGCAAATGTTTATCATGCCACAAAATCCGATGGTCACGAACTTGCAATTAAAGTGTACAAAACTTCTGTTCTAGTATTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
ttcttac putative branch site (score: 2)
ttgttttct putative PPT
ttttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgatccacctgaagcttttgtttacctgtttgtttttatgatgatgacatggtttggatcatcgactatatgtgatatcaagacaccacatttctgtttcttactgtgttgttttctaacagGCAAATGTTTATCATGCAACTAAATCTGATGGTCAAGAACTTGCAATTAAAGTATACAAAACATCTGTTTTGGTATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC