Sequence
atgc intronic sequence ATGC exonic sequence...ctagtttggtttcaactggtatttggtttctgctgtaatactttattttatttttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
Basic information
species | Glycine max |
transcript | GLYMA20G36530.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 6
-----ctagtttggtttcaactggtatttggtttctgctgtaatactttattttatttttttgcatctggtgcaa-tattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
| | | || | ||||| || | || ||| | ||| | || | |||||| | || | | | ||| ||| | || | ||||||| ||||||||||||||||||| ||||| ||| |||||| |||||||||| ||| ||||| || ||||| || ||||| || |||||| ||| ||
tgaggattctacgattggacctggtcaatgactattg--gtagtgatttgctggatgcct--gcatctcattcatctgctaatcgttt-attatgtaat-tttcagCTGAGACTGTAATATACAGAATCTTTTATTCCATAAATAGAGCTGGAAATGGCCATCTTACCCTCAGAGAGCTAAAACGTGGGAATTTAATTGCTGCGAT
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 6
-------ctagtttggtttcaactggtatttggtttctgctgtaatactttattttatt-tttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
||| | | ||| | || | ||| |||| ||| ||| | || | || | ||| | |||| | ||||| ||| |||| || ||||||||||||||||||| ||| | ||| ||||||||||| |||||| ||| || ||||| ||||| || |||||||| |||||| |||| |
aactcaacta-tctattttgttttaagatcagattt--gctg-aatgttttgaactgttgctaatgtttgctgtgtcacattcatttcttgatgtttt----cttcagCGGAGACTGTAATATACAGAATCTTTTACTCCATAAATAGATCTGGGAATGGTCATCTGACTCTGAGAGAGCTCAAACGTGGAAATTTAATTGCTGCACT
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------------------ctagtttggtttcaactggtatttggtttctgctgtaat--actttattttatttttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
|| || | | ||| || | | | ||| | | | | || | | || ||| || ||| | || | | ||| | | |||||||||||||||||||||||| ||||| ||||| ||||| ||||||||| ||| ||| |||| ||||| ||||| ||||| || |||| |||||
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatg-atccattgtaatgtatttga--aaaacttttggcaac--agCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatttttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
tttttca CT-rich tract
aatattcttaatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagtttggtttcaactggtatttggtttctgctgtaatactttattttatttttttgcatctggtgcaatattcttaatttgatttttcaacgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTTGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - -ctgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtgc