Sequence
atgc intronic sequence ATGC exonic sequence...cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccattcttgtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
Basic information
species | Glycine max |
transcript | GLYMA08G09360.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G01750.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgtctgccgtggtgttgattat-tggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccatt-cttgtttatttca-ctgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
| ||| || | | ||||| | | || || | | || | | | | ||| || | | || || | || | || | | | |||||||||||||||||| ||||| | ||||| ||||| || | ||||||||||| || || | ||| |||||||| |||||||||||||||||||||
--tttctttcg-gatcttgatcaaatccaaatgattatgtatcccctgtttctttgtaatgaaaacatatattttcactaatttactcatcatatccgactagGGTTTCTTCAACTTCACAGCTCGAAGGCCACAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G01220.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctga-gttttaaaatccattctt--gtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
| | || | | || || |||| | | | | | | | | | | | | | |||| ||| || || || ||| ||||| |||||||| || |||||| || |||| ||||| || | ||||||||| | || || | ||| |||||||| |||||||||||||||||||||
--tagcagcagccattttt-cccctgtttctgtatgtgatactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttcttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgtctgccgtggtgttgattattggaactg-tctcttaatttctttctcgtgtgtgg-tgctgagttttaaaatccattcttgtttatttcactgt-ctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
| | | | | || || | | | |||| | | | | || | ||| | | | || |||||| | | | |||||||||||||| | ||| | || ||||| ||||| | || ||||||||||| || || | ||| ||||||||||||||||||||||| ||| |
--acattaacatcataa-aagagttagaccaaatgtgataatatatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgtctgccgtggtgttgattat-tggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccatt-cttgtttatttca-ctgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
||| | ||| | | | | | | ||| || ||||| ||||||| | | || | || | || | || | | | ||||||||||||||| || ||||| | |||| ||||| || | ||||||||||| || || | ||| |||||||| |||||||||||||||||||||
-ttgaaaaaaaaag-attggtggtctagggccattgcttttattatttct-gtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
-cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccattcttgttt-atttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
||| | | | | | | ||| | | ||| | || | | || || || | || || ||| || |||||| ||| |||| |||||||| ||||| | | |||| ||||||||||||| ||||||||||||||||||| ||| ||||||||||||||||||||||| |||||||
ctttgcatttcctatttct--tctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
upper sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g04760.t01 (Vitis vinifera), 3'ss of exon 1
cttgtctgccgtggtgttgattattggaactgtctcttaatt-tctttctcgtgtgtggtgctgagttttaaaatccattcttgtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
| | | || | | ||| | || || || | || || ||||| | |||| || | | | || |||||| | | |||||||||| || ||||| | | |||| |||| || ||| | ||||||||||||||||| | ||| ||||| ||||||||||| ||||| |||||||
gctatacactgtctttctcattttcatttcttgctgatattgatcaatcatcaatgtgggattagtttttgaagtttgat-tgcttgatttcattatacagGGTTTCTTTAATTTTACTTCTCGAAGGCCTCGCCACCTACTGTACATTTTGGAGCTTGGATACAATGTTATGTATAATGATGTTGACATGGTATGGTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcgtgtgtggtgctgagttttaaaatccattcttgtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
ttcttgtttatttc CT-rich tract
ttttaaaatccatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccattcttgtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- tgtctgc
- - - - - - ggtgttg
- - - - - - - - - - - - - - -ctgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattct