Sequence
atgc intronic sequence ATGC exonic sequencegtactagtgttgtcaatttttgcatttgtagctctctggtacatcatttctctacttgaaagtagtatcacattttattcagctgtgggatgtatagagtaagtcaaatactttccagttctgaacatttgacaatttctgcagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
Basic information
species | Glycine max |
transcript | GLYMA17G05390.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015190_T01 (Zea mays), 3'ss of exon 8
----------------------gtactagtgttgtcaat----ttttgcatttgtagctctctggtacatcatttctctacttgaaag--tagtatcac----attttattcagctgtgggatgtata---gagtaagtcaaatactttccagttctgaacatttgacaattt---ctgcagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
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gtatagttctaattgtggcaccaccccaccattgcctatgctacattatatgtgtgcttatttgctgcagaaaagtaaaagataagaggttaacataattttgacttgctttaccaatttcatctttaagtgtttctttcaactatttttctgaacactagagttgatgttatgaataacagGCAGAGATTGAAGCTCATACTAAGCCAGGCACTGCGAATATATATGTTCACTATGGACAAAACAGGCCAAAAGATGCAAGCATCATTGGTCAGAGTGATA
upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 8
gtactagtgttgtcaatttttgcatttgtagctctctggtacatcatttctctacttgaaagtagtatcacattttattcagctgtgggatgtatagagtaagtcaaatactttccagttctgaacatttgacaatttctgcagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
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----------------gtattccatgcttaatgcacgtgcacactatagtttggttatccgtcaaagttg---ttaattgttctttgtctttccttgtgtcagctaa-tattttcttgctcc---tgctttatgat-----cagACAGAGATTGAAATGCATGCAAAGCCTGGGTCTCTATCTGTCTATGTTCACTATGGGCAAAGCAGGCCGAAGGATGCAAAACTTCTTTCCCAGAGTGATG
upper sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 8
gtactagtgttgtcaatttttgcatttgtagctctctggtaca-tcatttctctacttgaaag--tagtatcacattttattcagctgtgggatgtatagagtaa------gtcaaatactt-tccagttctgaa--catttgaca-atttctg------cagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
||| | || || |||| ||| ||| | || | | ||| | | | | | || || | || | | |||| | || | | ||| ||||| |||| |||||| ||| | | || | || ||||||||||||||||||||||| || ||||| ||| ||||| | |||||||| ||||||||| |||| || |||||||||| ||| ||| |||||||||
gtagccattttccca-ttttgatctttacttttcttagatatacttattgccattttccactgcttattaaaggagttggtaatgtaatgggtatcacaggctcaccagcaatcatgtacttctccatttctgagattattctaaacatctgtgtgttgacagGCAGAGATTGAAACTCATGCTCAACCTGGTTCTTTGTCTGTTTATGTTCATTATGGACAAGGTAGATTGAAGGATGCAAAAATTCTAGCCCAAAATGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtatagagtaagtcaaatactttccagttctgaacatttgacaatttctgcagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
atttgac putative branch site (score: 4)
tttctgc putative PPT
aaatacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactagtgttgtcaatttttgcatttgtagctctctggtacatcatttctctacttgaaagtagtatcacattttattcagctgtgggatgtatagagtaagtcaaatactttccagttctgaacatttgacaatttctgcagGCAGAGATTGAAACTCATGCACACCCTGGGTCTCTGTCTCTATATGTTCACTATGGACAAAGTAGGCCAAAAGATGCAAAAAGTCTCGCCGAAAATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG