Sequence
atgc intronic sequence ATGC exonic sequence...ttatcttgccgttggatcaggagtagcttcaaccctccgtaagtggatttgctcttccaacctagaggtatcatgttgatgacttttatgttccctagagGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g34970.1 (Oryza sativa), 3'ss of exon 2
--ttatcttgccg--ttggatcaggagtagcttcaaccctccgtaagtggatttgctcttccaacctagagGTATCATGTTGATGACTTTTATGTTCCC-TAGAGGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
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acttgtgtttctgtattgatactacagtagtgatgttcatatcgttttaaggctactactagaaacaaaa--tttcctgat-atattggctatgttttggtagAGGTATCATGTTGGACAATCACTGGAGAAAGGCAGGCTGCACGAATCAGGGCATTGTATCTCAAGGCAATACTTAGACAGGACATTGCCTTTTTTGACAA--
upper sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g35030.1 (Oryza sativa), 3'ss of exon 3
ttatcttgccgttgg-atcaggagtagctt---caaccctccgtaagtggatttgctcttccaacctagagGTATCATGTTGATGACTTTTATGTTCCCTAGAGGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
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acaacgtgctactagtacttgcagttcttttgtcaggagctttttattggaaatattattagaaacaatgcttacttgattcattatgacaat--ttggtagAAGTATCATGCTGGACAATCACTGGAGAGAGACAGGCAGCACGGATTAGGGCGTTGTATCTCAAAGCAATACTGAGGCAGGATATTGCCTTTTTTGACAA--
upper sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ12488 (Selaginella moellendorffii), 3'ss of exon 2
ttatcttgccgttggatcaggagtagcttcaaccctccgtaagtggatttgctcttccaacctagagGTATCATGTT-GATGACTTTTATGTTCCC-TAGAGGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
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--------------------------------------gtaacttg-ctcgcttggacgacctgcactgctcctaacagatggatggtgcgctaatgcagAGCTGTGCTGTTGGATGTGCACGGGAGAGCGGCAAGCAGCTCGTATCAGGAGCCTGTATCTCAAGGCCATTCTGCGGCAGGACATCCCATTCTTTGACAC-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgctcttccaacctagaggtatcatgttgatgacttttatgttccctagagGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
tgttgat putative branch site (score: 4)
cttttatgttccct putative PPT
ttttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcttgccgttggatcaggagtagcttcaaccctccgtaagtggatttgctcttccaacctagaggtatcatgttgatgacttttatgttccctagagGTATCATGTTGGACAATCGCCGGAGAAAGACAGGCGGCACGAATCAGAGCCATGTATCTCAAGGCAATTCTGAGGCAGGACATTGCGTTCTTTGACATGG
- - - -gccgttg
- - - - - - - - - - - - agcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat