Sequence
atgc intronic sequence ATGC exonic sequencegttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgactcttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
Basic information
species | Glycine max |
transcript | GLYMA12G22240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 3'ss of exon 5
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgta-agagtgtacttaaaattaattaaatttaaatatcacttgactcttaatatt-ttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
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--------------------------------------------------------------------------------------tattctgtagcatctcatgttcatactgtgttttcccctttatatgcttgtctatctgtctagtttagaggctatttgatgtgacccttttgttgtg--cagACCGAGATGACTACTGCTGAAAGAGAGCTTGATCACAACACAAATTATGACTGGAATAGAATACAAGAAAGTGGCAAAGATGCCGAACTTTTATACGGCC
upper sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107696_T02 (Zea mays), 3'ss of exon 9
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgactcttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
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---------------------------------------------------------------------------------tatgttacagctg-atgcataatacagtttttttcctgct-tgacatgtacatagaggcaattttatgcttggccacattgttta--taaatttgttct-tgcagACTGAGATGACTACTGCTGAGAGGGAACTTGATGCTAACACAAATTATGACTGGAATAGAATACAAGAAAGTGGAAAAGACGCTGAGCTTCTGTTTGGAC
upper sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgact-cttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
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----------------------------------------------------------------------------tttgtactgccttgatcatcatctttgc-taaagatat-cccatgctggttttaatctgaataatgttaactttcttgaaatgtt----tgctacaattttca-----cagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACAAATTTTGATTGGAACCGTATACAAGAGAGTGGAAAAGAATTGGTGCCAGTTTTTGGAC
upper sequence: GLYMA12G22240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 3'ss of exon 5
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgactcttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
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------------------------------------------------------------------------ttttttttttttgataaat-gatagttgttgcttgagaa-----tcaacattgttta--cttacatttcattaaaccttaagctcaatata------cattttcttgtttccagACTGAAATGACTACTGCTGAAAGGGAACTTGACCAGAATACCAATTTTGATTGGAACCGAATTCAAGAAAGTGGACAAGAAGTTGAACCACTATTTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaatatcacttgactcttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
tcttaat putative branch site (score: 3)
tttcttat putative PPT
actcttaatattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaattatttatcttgaaatgatacttttcacgcacaataaaaaatatattaattattaatcttgagtataaacttttgtcttgttactccaacaggcatggcgtaagagtgtacttaaaattaattaaatttaaatatcacttgactcttaatattttaaactggtccaatttcttatattcagACTGAAATGACAACTGCTGAAAGAGAACTTGATCAAAATACGAATTTTGATTGGAATCGAATCCAAGAAAGTGGACAAGAAGTAGATCCAATTTTTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT