Sequence
atgc intronic sequence ATGC exonic sequence...tggattgattttgtactccatttgtgctggtgtggatgtgattgtctggattgtcaatttatctactctgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 2
tggattgattttgtactccatttgtgctg-gtgtggatgtgattgtctggattgtcaatttatctactc-----tgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
|| | || | | | | || || || ||| || | ||| || | | ||||| | || ||| ||| || ||| ||| || ||| || | | | |||||||||||||||||||| |||||||||||||| || | | || ||| | || ||||||||||| | || | ||| |||||| |||
---gtttttcttctgtcctaatggttttgagtatggttgag-ttggctaaggtttaaatttttatatgggttggtgtccttcacttcattattg--ttacttccagAATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCAGGCGTTGCCACTACACTGTTACCACCTCAAGAAGTGACCATGAAACTTGAAGCTATG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15473 (Selaginella moellendorffii), 3'ss of exon 2
tggattgattttgtactccatttgtgctggtgtggatgtgattgtctggattgtcaatttatctactctgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
| || || ||||| |||| | | || | || | ||| | | ||| |||| | |||||||||| ||||||||||| |||||||| ||||| || | || || | || ||||| | | | || || || |||
---------------------------------------gtatgcctcgattg--aattcaagttcttcgctgata----atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 2
tggattgattttgtactccatttgtgctggtgtggatgtgattgtctggattgtcaatttatctactctgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
| || || ||||| |||| || | || | || | ||| | | ||| |||| | |||||||||| ||||||||||| |||||||| ||||| || | || || | || ||||| | | | || || || |||
---------------------------------------gtatgcctcgattg--aattcatgttcttcgctgata----atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggattgtcaatttatctactctgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
ttttaat putative branch site (score: 3)
tgttcctt putative PPT
tacttattttaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggattgattttgtactccatttgtgctggtgtggatgtgattgtctggattgtcaatttatctactctgtacttattttaattgttgtgttccttatagGACGATAAATGGACTTCTTAAAACTGCCCAAGGTGTCCCTCCTGGTGCAACGACCACAGTTTTGCCACCTCAAGAGGAAACACTAAAATATGAAGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - tttgtgc
- - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - -ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg