Sequence
atgc intronic sequence ATGC exonic sequence...tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
Basic information
species | Glycine max |
transcript | GLYMA10G43050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G14810.1 (Arabidopsis thaliana), 3'ss of exon 2
tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
||| || | || | | || ||| | || ||| | | | | | | | | | || ||| |||||||| || || || ||||||||||| || |||||||| || || ||||| ||||| |||||| ||| |||||| || || |||| | || |||| |
--------------gtaa--gtctcaaattcaatatat---caattaagaatctttacatggaaacagagttatctaatctcgcgagttc--tttcacagGTTAAGGCGTTTAGAGAAAGGAGAGCTCTGGCTTTGACCTTAAACGATACAAAAACAGCAGTGGACAGACTTCACCGTATAATCAACGTGGTAATTGGCA
upper sequence: GLYMA10G43050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G14810.2 (Arabidopsis thaliana), 3'ss of exon 3
tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA------
||| || | || | | || ||| | || ||| | | | | | | | | | || ||| |||||||| || || || ||||||||||| || |||||||| || || ||||| ||||| |||||| ||| |||||| || || |||| | || |||| |
--------------gtaa--gtctcaaattcaatatat---caattaagaatctttacatggaaacagagttatctaatctcgcgagttc--tttcacaggttaagGCGTTTAGAGAAAGGAGAGCTCTGGCTTTGACCTTAAACGATACAAAAACAGCAGTGGACAGACTTCACCGTATAATCAACGTGGTAATTGGCATTATAA
upper sequence: GLYMA10G43050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G53470.1 (Arabidopsis thaliana), 3'ss of exon 2
tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgctta--tatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
|| || | || | | || | | || |||| ||| | | | || | ||| || | || | ||||||||||||| || ||| | |||||||| ||||| ||||| || ||||| ||||| |||||||||| ||||||||||| | || | | || | |
--------------------gtaagtgtttgttttcagttcaaatttcaaaaactttcttacgtatgacaatgatgctagattcttaaatct--ttttctagGTTAATGCCTTTAGAGAACGAAGAGCACTAGCTTTAACATTAAACGATACAAAAACAGCAGTGAACAGGCTTCATCGAATCGTTGATGTATTGGTCAGCA
upper sequence: GLYMA10G43050.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g03030.t01 (Vitis vinifera), 3'ss of exon 5
-tttatagcatttacataacggttttaatt----gatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
| ||| | | | | |||| ||| | ||| || | | ||| || | || | || | | || | ||||||||||| ||||| ||||||||||||||||| |||||||||||||| || ||||| || || ||||||||||||| |||| | ||| || ||||| |
ccacaccccatggatgcatgaatatgaatttgcagattctaacacacagcacctatcttttactcgctga---ttgataatg--tgtaagtcttggttgtttcagGTTAATGCTTTCAGAGAAAGGAGAGCACTTGCCTTGACATTGAATGACACAAAAACAGCCGTTAACAAACTTCATCAAATGGTGAATGTTGTAGTTTTCA
upper sequence: GLYMA10G43050.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g02980.t01 (Vitis vinifera), 3'ss of exon 3
------tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
| || | || | | | | || ||| | ||| ||| | | | ||| || | || | || | || || | ||||||||||| ||||| |||||| ||||||||||||||||||||||||| || ||||| || || ||||||||||||| |||| | ||| || |||||| |
ccacacctcatgg-atgcataaatatgaatttgcagattctaacacgcagcacctattttttactcgctga---ttgataatg--tgtaagccttggctgtttcagGTTAATGCTTTCAGAGAAAGGCGAGCACTTGCTTTGACATTGAATGACACAAAAACAGCCGTTAACAAACTTCATCAAATGGTGAATGTTGTAGTTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
atttaac putative branch site (score: 3)
cttccc CT-rich tract
ttatatagtatttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatagcatttacataacggttttaattgatgtttacatgcaactgtttatgtttgcttatatagtatttacaacagttccttgcatttaacttcccagGTTAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGATACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGGAA
- - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc