Sequence
atgc intronic sequence ATGC exonic sequence...tattccatccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcacatgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
Basic information
species | Glycine max |
transcript | GLYMA13G17610.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 10
tattccatccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcacatgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
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---------gttagcttacttctttgaggttgcttatttttatttttt-----tctttgttttgatt--ttattcgtagccattct--------cttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 11
tattc-catccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcaca-tgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
| || ||| | | || | ||||| | | || | | |||||||| | || | | | | | | | |||||| |||| || ||||| || |||||||||||||||||||| || ||||| ||||||||||| || || || |||||||||||||| || || || ||||
tgttgacattagattgttatttatgttgcattcattgaaggtcctttctgttggctg--attttgaccaattttctgcaataaatatgtttgcaatatgcagGGTATGTTAGAAGGAGTTAGTCACTCATTTACAAAGAACTTTCACTTTATAGATTCAGTGAAAGCCTACCTCTCATATGCATTGTTGCGGGCGTCGGTTT
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 12
--tattccatccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcacatgcttcttatgttattttt-cagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
||| | | | ||| | || || | | || | | | | || | ||| |||| | || | | | || || |||||||||||||| || || ||||| |||||||| | ||||||||||| ||||| ||||| || ||||||||||| ||||| || |||| || || ||||
tttatatcccttgtatgcttttgggtctgcctt-aaggtgccctttttctaata--tatttctttctctgtgtttttacttatataaaaaaaaatgattgcagGGTTTGTTGGAAGGTGTTAGCCATTCATTTACGACAAACTTCCATTTCATTGACTCAGTAAAAGCATATCTTTCTTATGCTTTACTACGGGCATCGGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgacagttactattttgactgttcagtcacatgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
ttttgac putative branch site (score: 3)
ttatttttc putative PPT
ttcttatgttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattccatccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcacatgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -tccatcc
- - - - - - - -cttccca
- - - - - - - - - - - - - - - tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct