Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 3
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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gtaagattcttattcagttctgttttg--ttacacttgtaatatgtcgaacctctctagcttcactgtccc------tttggtcaaattagatgcatt-ttagtgaagtcagtg------------atcctaattttattgatgacaaaatttgttttgctt--ctagCCGAGAGTTCACGCATCGAGCGAAGTCAGTTTCTATGGCTAAATTTACTGCACAGGAAGTTAGTGCCCTTCAAGAAGGAGGAAATGAG
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtga-attattgggcac-accagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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------------------------------------------------------------cattttgtttaa-aaaatattgga-gatagaataatatcatttctttctagtgttcacttttccttgaatgaaagtcaactgcttt-------ttgttttgattta-tagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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--------------------------------------------------------tttaaaatatattgtgctgtactagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgtttt-----------ttgtgttgattta-tagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 3
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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-------------------------------------------------------------------attgtaattattttaaatattctattgtactag-agataggacaatgttgtttcagacttcagtttactttctcctcaactgccttttgtttaatttccagCCGAGAGTTTACACATCGGGTAAAATCAGTTTCAATGGCTAAATTTAGTGCACAGGAAGTTAGTGCACTTCAAGAAGGAGGAAATCAG
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G04420.2 (Glycine max), 3'ss of exon 2
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggc-acaccagtcccctggtgaaat-atgccagtctttttcctaatataaatcactttgttt---tcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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-------------------------------------------------------------------------tgtccaaattgtaattattttaaatattctgttgtactagagataggacaatgttgtttcagtttcctttcttctcaactgccttttgtttaatttccagCCGAGAATTTACACATCGGGTAAAATCAGTTTCAATGGCTAAATTTAGTGCACAGGAAGTTAGTGCACTTCAAGAAGGAGGAAATCAG
upper sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
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-------------------------------------------------------------tgttacgaggatggtgtgttg-acaattgggtctgtt--tataaatattggctttatcaacaattgtgtg---ctctgacttattttttatttcataacaattc-agTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
tcctaat putative branch site (score: 2)
tcactttgttttcct putative PPT
taatataaatcacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG