Sequence
atgc intronic sequence ATGC exonic sequencegtaattagttctataaattattattaatcactggcaggatacttacacaggttaataaacttattattattttgatagctactctttaccttagtatttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA
Basic information
species | Glycine max |
transcript | GLYMA03G04330.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
--gtaattagttctataaattattattaatcactggcaggatacttacacaggttaataaacttattattattttgatagctactctttaccttagt-atttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA
| || | | | | || | || | || | ||| | | ||| || || | ||||| || || || | || | | || | ||||| | | || ||| |||||||| || || || ||| | |||||||||||||| ||||| |||||||||||||| |||||||| || || | ||||||||||||||||||
gtatccttgactatgtcatttttattttgaagttcatagattgcttc-----gctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
upper sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S42_132V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaattagttctataaattattattaatcactggcaggatacttacacaggttaataaacttattattattttgatagctactctttaccttagtatttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA
||| | || | | ||| ||| | | |||| | || |||| ||||| || | | | ||| | || || || | || | || ||| | | || || || | || || || ||||| ||||| || ||||||||||| |||||||| ||||| | |||||||||||||||||
gtatcctttcagatttcatgcattcaatttctgatttcgtggg-atgagggtttttgggatttttatgattttcttaaa-agggtacagttta--aattgtgta---cttgacaatgtattttagTATGCAAACCACCATCACTCCCTTGTTCGAGAAAATGCTGAGTGCCAGCGATGCTGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGTGCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatagctactctttaccttagtatttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA
ccttaac putative branch site (score: 3)
ttagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattagttctataaattattattaatcactggcaggatacttacacaggttaataaacttattattattttgatagctactctttaccttagtatttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG