Sequence
atgc intronic sequence ATGC exonic sequence...gcttttattactattttatagtatcctattatatggtgttcactttgcaacttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
Basic information
species | Glycine max |
transcript | GLYMA17G15320.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 8
-gcttttattactattttatagtatcctattatatggtgttcactttgcaactt--ttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
| |||| || | || | | || ||| | | | | | ||| || || | ||| ||| || ||| ||||||||||||||| |||||||| ||||| || ||||| ||||||||||| |||||| || || ||||| || ||||| |||| ||||| | ||||| |
tgagtttacacgcatagc-tggtccaacagtctagccagtttatataacgagtgaattacacaattttcattgttctcaaacctgtttttttttaat--gcagGATGGAATTGAAGAATGCCGAAAACTCTGTGGTGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTT
upper sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G052389_T02 (Zea mays), 3'ss of exon 8
gcttttattacta-ttttatagtatcct-attatatg-gtgttcactttgca-acttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
| | | || | | || || | | | ||||| | || || | || ||| | ||| ||| || | | || || ||||||||||| |||||| |||||||| || || || ||||| ||||||||| | ||||||||| || |||||||| ||||| ||||| |||| | ||||| |
gtagtaggttctggtctgatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagat---ttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT
upper sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 8
gcttttattactattttatagtatc-ctattatatg-gtgttcactttgca-acttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
| || | | || || | | ||||| | || || | || ||| | ||| ||| || | | || || ||||||||||| |||||| |||||||| || || || ||||| ||||||||| | ||||||||| || |||||||| ||||| ||||| |||| | ||||| |
tagtaggttctggtctgatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagat---ttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT
upper sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
---gcttttattactattttatagtatcctattatatggtgttcactttgcaacttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
|| || | | || || |||| || | | | | | | | || ||| | ||| | | | || ||| |||| ||| | ||||||| ||||| |||||||| |||||||| ||||||||||||||||| || || ||||| || || ||||||||||| || || | ||| |||| ||||
tgaactattgagtcctgatcttaatagcctacaat-tcaagcaagttatactagtaggtatgctt-ggagtgctgctaattttctgttcactttgatt-gtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaacttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
ttttaat putative branch site (score: 3)
ttttaattctttgaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttattactattttatagtatcctattatatggtgttcactttgcaacttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT
- - - - - - - - - - - - - - - -tatggtg
- - - - - - - - - - - - - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaaa