Sequence
atgc intronic sequence ATGC exonic sequence...aattgtgcgaagatgtttatctatttgcattgcttggtatgtggtaattgtgtaattggtgattttggggtttatgtgcttactacatgcaactttttagGATGAAACGGGGGTGTACAAGAACCTCTTGCAGGAAATTGCGCAGAGGGTAGGGGCGCCGTTGCCGCAGTATTTTACATTCAGGTCAGGGTTAGGACATT
Basic information
species | Glycine max |
transcript | GLYMA12G08070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08070.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g02810.t01 (Vitis vinifera), 3'ss of exon 1
aattgtgcgaagatgt-ttatctatttgcattgcttggtatg--tggtaattg--tgtaattggtgattttggggtttatg-tgcttactacatgcaac--tttttagGATGAAACGGGGGTGTACAAGAACCTCTTGCAGGAAATTGCGCAGAGGGTAGGGGCGCCGTTGCCGCAGTATTTTACATTCAGGTCAGGGTTAGGACATT
| || |||| || | ||| ||| |||| | | |||| | | ||| | ||||| || || | || | || | || || ||||||||| ||||| |||||||||||||| || ||||| ||||| || || ||||| || || ||||| || || || ||||||||||| | || ||
-----tttcaatatgtgttgtgtatccatattccttgatctacttggttcacagctatgattagatattttt---ttcgtgatactgattaagttttaccattgttagGATGAGACGGGAGTGTACAAGAACCTTTTACAGGAGATTGCACAAAGAGTAGGAGCACCATTGCCTCAATACACAACTTTCAGGTCAGGCCTTGGGCACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtgtaattggtgattttggggtttatgtgcttactacatgcaactttttagGATGAAACGGGGGTGTACAAGAACCTCTTGCAGGAAATTGCGCAGAGGGTAGGGGCGCCGTTGCCGCAGTATTTTACATTCAGGTCAGGGTTAGGACATT
tgcttac putative branch site (score: 2)
cttttt putative PPT
aacttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgtgcgaagatgtttatctatttgcattgcttggtatgtggtaattgtgtaattggtgattttggggtttatgtgcttactacatgcaactttttagGATGAAACGGGGGTGTACAAGAACCTCTTGCAGGAAATTGCGCAGAGGGTAGGGGCGCCGTTGCCGCAGTATTTTACATTCAGGTCAGGGTTAGGACATT
-attgtgc
- - - - - - - - - - - -tttgcat
- - - - - - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - - - - -tgtggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - attggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgc