Sequence
atgc intronic sequence ATGC exonic sequence...aagaaccacataacccttcaggaatgacagttttatggacatactgtcgataatttaatgaagcctatttaaatgctaattcatgtgctatcctccacagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
Basic information
species | Glycine max |
transcript | GLYMA20G03250.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 3
aagaaccacataacccttcaggaatgacagttttatggacatactgtcgataatttaatgaagccta----tttaaatgctaattcatgtgctatcctcca-cagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
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-----ctatatttaatttcaccaatagcttattgattcatagagttccctttattttagaaatattaagattggatatgctacttttgtaattgcaatcaagtagGAGCCAGATGCTGCCCTTGGGAATGGTGGTCTAGGCCGGTTAGCTTCCTGTTTCTTGGATTCTCTGGCAACCCTAAATTATCCAGCATGGGGATATGGAC
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G074158_T02 (Zea mays), 3'ss of exon 3
aagaaccacataacccttcaggaatgacagttt--tatggacatactgtcgataatttaatgaagccta---tttaaatgctaattcatgtgctatcctccacagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
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-gttattctatgaaattttggatataaaactttatgatgcctaaactgctttggagttag-aaatcctaaggtttggatgatgctgtac-tgctatgaa--acagGAACCAGATGCTGCCCTGGGCAATGGTGGTTTAGGCCGCCTGGCTTCTTGTTTTTTGGATTCTTTAGCAACATTAAATTATCCAGCATGGGGATATGGAC
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g00730.t01 (Vitis vinifera), 3'ss of exon 3
------aagaaccacataacccttcaggaatgacagttttatggacatactgtcgataatttaatga---agcctatttaaatgctaattcatgtgctatcctccacagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
| | || | | ||||| | ||| | | || | |||| | | || | ||||||| || ||| || | | ||||| || |||||||||||||||||||||||| |||| |||||||||| ||||| ||||||||| ||||||| | ||||| || || ||||| |||||||
gtaaatatggactgttttatttatcagggtgccctctttgtcacttgttgtctcaaagatttgaagcgttagggtgtttaaattctg--tcaattgatggct---gcagGAACCAGATGCTGCCCTTGGGAATGGGGGACTAGGAAGGCTTGCTTCCTGCTTCCTGGACTCCCTGGCAACACTAAATTATCCGGCTTGGGGCTATGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcgataatttaatgaagcctatttaaatgctaattcatgtgctatcctccacagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
tgctaat putative branch site (score: 2)
ctatcctcc putative PPT
tatttaaatgctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaccacataacccttcaggaatgacagttttatggacatactgtcgataatttaatgaagcctatttaaatgctaattcatgtgctatcctccacagGAGCCGGATGCTGCCCTTGGGAATGGGGGATTAGGTCGGCTTGCTTCTTGCTTTCTGGACTCCTTGGCAACCTTGAATTACCCTGCATGGGGATATGGAC
- -aaccaca
- - - - - - -cccttca
- - - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - - - -tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc