Sequence
atgc intronic sequence ATGC exonic sequencegtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g41850.1 (Oryza sativa), 3'ss of exon 5
gtgagcc-ctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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gtgagcctctagtgtctttttgtaaaatg--aacttaacaaacctttactgtgttatttgatctactttatgtaa-------------atagggtat----aattaaatggtt-------gactttctgctgatgccttcttttaatattgggtgcagTTTGTCCAACAACTTTGAAACGGATATGCCGGCATCATGGAATTTCACGATGGCCATCTCGCAAGATAAACAAGGTTAATCGTTCATTAAAGAAGATTCA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgc--agctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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------------------------------------------------ttcaat-ttcattgtccaaaaaagatgttcaatatttctgaaaggaaattctt--gttaattg-----gaaaaagtttattcttaacaaatgtttctt--ctttgat-cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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------------------------------------------------tatgatttt----atcttaaagttaagatgtaagacatttctgaaagg--taattctagttaataaagacagatttatcgttaacaaacatttct---tctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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----------------------------------------------tctatgat-tttat----cttaaagttatgtta--aacatttctgaaagg--taattctagttaacaaagacggatttgtcgttaacaaacatttttttatttga--acagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G03220.1 (Glycine max), 3'ss of exon 7
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgc--agctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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------------------------------------------------tgcaat-ttcattgtccaaaaaatatgttcaatatttctgaaaggaaattctt--gttaattga-----aaaaagtttattcttgacaaatgcttctt--ctttgat-cagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G59580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctg-acacttgcctataaacaccatt---gcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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-------------------------------------------------------------gtga-gaaactagtactagtagtgctctttgcttgtttcccttacaagattattcaattgctgatccttggatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccat-tgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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-------------------------------------------------------------------------------------------------------------gttagcacacaaacta--tctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
upper sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0094g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
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------------------------------------------agtagtcccaacaact--agta-taaataagatgttatt-tggaagaagaagttggcaaactgtgtagtc-tgatattga----ttttgat-tttatctttg-----ttttacagTTTGCCCCACTACACTCAAAAGAATCTGCAGACAACATGGGATATCAAGATGGCCGTCCCGCAAGATCAACAAGGTGAACAGATCACTGAGGAAGATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
ttctgac putative branch site (score: 2)
attatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG