Sequence
atgc intronic sequence ATGC exonic sequencegtcagagctgccgctgagcttgccaatgctttacatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G119894_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g18670.1 (Oryza sativa), 3'ss of exon 5
--------------------gtcagagctgc-cgctgagcttgccaatgctttacatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
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gttagaagtctactctatatgcaagttttgtgtttccagtattcagaatttttagatcattgggcataacatactgagatttct---tccttctccttgccaatattt-acagGGCCTTGATACTTCAGTTGGTGAACATGGGACTCAGCTTTCTGGTGGGCAGAAGCAAAGAATTGCCATAGCAAGAGCAATTCTAAAAGATCCAAGGATCC
upper sequence: GRMZM2G119894_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ10214 (Selaginella moellendorffii), 3'ss of exon 6
gtcagagctgccgctgagcttgccaatgcttt-acatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
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---------------------gtaaatgctttcaaagttttcatggaa----agttccatagttatcttttgtttgcttccaacctgta--agGGATTCGACACACAAGTTGGAGAGCACGGGACTCAGCTTTCTGGCGGACAGAAGCAAAGGGTGGCCATCGCTAGAGCTATACTAAAAAATCCTCGCATTC
upper sequence: GRMZM2G119894_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ10284 (Selaginella moellendorffii), 3'ss of exon 6
gtcagagctgccgctgagcttgccaatgctttacatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
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-----------------------------------------gtgagaattcaatccggtcattaagg--attgcggttaagtgttttggcagGGTTACAGCACGCACGTTGGAGATCATGGAACACAGCTTTCGGGAGGTCAGAAGCAGAGGATCGCAATCGCCAGAGCTATCCTCAAGAACCCTCGCATTC
upper sequence: GRMZM2G119894_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ12488 (Selaginella moellendorffii), 3'ss of exon 6
gtcagagctgccgctgagcttgccaatgctttacatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
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-----------------------------------------gtgagaattcaatccggtcattaagg--attgcggttaagtgttttggcagGGTTACAGCACGCACGTTGGAGATCATGGAACACAGCTTTCGGGAGGCCAGAAGCAGAGGATCGCAATCGCCAGAGCTATCCTCAAGAACCCCCGCATTC
upper sequence: GRMZM2G119894_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ12574 (Selaginella moellendorffii), 3'ss of exon 6
gtcagagctgccgctgagcttgccaatgcttt-acatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
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---------------------gtaaatgctttcaaagttttcatggaa----agttccatagttatcttttgtttgcgtccaaccttta--agGGATTCGACACACAAGTTGGAGAGCACGGGACTCAGCTTTCTGGCGGACAGAAGCAAAGGGTGGCCATCGCTAGAGCTATACTAAAAAATCCTCGCATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
ttctgat putative branch site (score: 3)
tttaatttctcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagagctgccgctgagcttgccaatgctttacatctctctcggtggttcagtttaatttctcaatctgttctgtttctgatatttcacagGGTTTCGATACCTCGGTTGGCGAGCATGGGACACAGCTCTCTGGTGGACAGAAGCAGAGGATCGCCATCGCAAGGGCTATTCTGAAAGATCCAAGAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT