Sequence
atgc intronic sequence ATGC exonic sequence...ttttaactctaaaatctgagcatgataaaaccattgaaaatatcaatttcaggattttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
Basic information
species | Glycine max |
transcript | GLYMA17G05350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g42020.1 (Oryza sativa), 3'ss of exon 3
---ttttaactctaaaatctgagcatgataaaaccattgaaaatatcaatttcaggattttttgtacttcactaatttgatcatggtgattggtttgtga-cagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
| || | ||| | || | | || | | | ||| ||| | || ||| ||||||| || ||||| |||||||||| ||||| ||| || ||||||| ||||| |||||||| ||||||| || |||| ||||||||||||||| || || |||| || || |||||
ctatactagtgtagcacactggccttgttttggacttttttctt-ttggcatggtgatgacatgtttgttgctg--ctgacggtggtgat-ggcgtgtgagcagTGAATGCAAATGAATGCCTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCAAAGTAGAGCAAGAAGTGGGTTCCTCCACACACGCCTTCTT
upper sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
ttttaactctaaaatctgagcatgataaaaccattgaaa-atatcaatttcaggat-tttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
|| | | | ||| |||| | ||||| |||| | || | | | |||| ||| || | || | | || || |||| | |||||||||| ||||||||||| ||||||| ||||| |||||||| ||||||| || |||||||| ||||| ||||| | || | || |||||
--ttctcatggagctatgatgttgatcttgtctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
upper sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
ttttaactctaaaatctgagcatgataaaacc--attgaaaatatcaatttcaggattttttgtacttcactaatttgatcatg-gtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
| | | | | ||| | || | | || ||| || || ||||||| ||| | | ||| ||| | || | || || |||| ||| | |||||||||| ||||| ||||||||||| |||||| ||||||| |||||||| || ||||||||||| || ||| | || |||||||| ||
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggact--aatgttttaatcctttgttgtatacttttg-cagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
upper sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 3
--ttttaactctaaaatctgagcatgataaaaccattgaaaatatcaatttcaggattttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
||| | | | | || |||| | | | | ||||| || || | | | | | || | ||| | | ||| || |||| |||||| | |||||||| ||||||| ||||||||||||||| ||||||||||||| ||||| |||||||||||||| ||||| |||||||| |||||
cctttccaaattggacaaaaattataataataataataataatatttatgattggttgataaatgatac-taaaatggatttatacgggtaattt-tggcagTAAATGCGGACGAGTGCTTAATGACAAGGATGCAAGAGATGTCATTGGATTATCATTTTACAGTGGAGCAAGAAGTTGGATCAGCTACTCATGCCTTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcaggattttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
attttttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttaactctaaaatctgagcatgataaaaccattgaaaatatcaatttcaggattttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggtg