Sequence
atgc intronic sequence ATGC exonic sequencegtgttagcaattgcattgttttagtttgtgtttcattcttttcttgaagtatttacttagtgggataaggcttttgttgttattgttgtttctattgtcttgaagtagtaattactaaagcaatgatagcttttcattttgaacaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT
Basic information
species | Glycine max |
transcript | GLYMA10G09180.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G09180.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g02110.t01 (Vitis vinifera), 3'ss of exon 1
gtgttagcaattgcattgttttagtttgtgtttcattcttttcttgaagtatttacttagtgggataaggcttttgttgttattgttgtttctattgtcttgaagtagtaattactaaagcaatgatagcttttcattt-tgaacaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT
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-----------------------gtctgtatcacaccacttttttcttttttttcttttttc--tttacttcccctttgtt-ttgtgttttatgttcactt--agcaaatgtcaccctttttccttttttttttttttggtaaacagCCAAAGCTTTGTTTGGACAGGATGAATGGTATTTCTTTACACCAAGAGATAGGAAGTATCCAAATGGAGTGAGGCCTAATAGAGCAGCAGCTTCAGGTTA-
upper sequence: GLYMA10G09180.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgttagcaattgcattgttttagtttgtgtttcattcttttcttgaagtatttacttagtgggataaggcttttgttgttattgttgtttctattgtcttgaagtagtaattactaaagcaatgatagcttttcattttga--acaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT
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----------------------------------------------tagtatc-atctcacaaattgaaggcagcgcctaaactatccaacataacga-ttcagttgtaaaatactgagctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgtcttgaagtagtaattactaaagcaatgatagcttttcattttgaacaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT
tactaaa putative branch site (score: 1)
cttttcatttt putative PPT
tagtaattactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttagcaattgcattgttttagtttgtgtttcattcttttcttgaagtatttacttagtgggataaggcttttgttgttattgttgtttctattgtcttgaagtagtaattactaaagcaatgatagcttttcattttgaacaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA