Sequence
atgc intronic sequence ATGC exonic sequencegtgaggatttatcgcgcctcccacctcagatccaggggaattcgtgtttttttgctgcgaattttggggttatcctactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
gtgaggatttatcgcgcctcccacctcagatccagg-ggaattcgtgtttttttgctgcgaattttggggtta-tcctactctcactcagtgcgcctg-----------------cacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
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gtgagtgttc-cggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatttatcgcgcctcccacctcagatccaggggaattcgtgtttttttgctgcgaattttggggttatcctactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
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---cagatttg----gcctcctacttgttgttaattgctattggt-ttcatgtact-cgaggct-ggctttcatttctgcttttttgatccgacgaattgtatctg---gcagATGCTTGGTGATGAAATCGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGATTTTGTGGCTATTAAGCAGGTCTCACTGG
upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatttatcgcgcctcccacctcagatccaggggaattcgtgtttttttgctgcgaattttggggttatcc--tactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
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-----------acatacgaactagcaacaatcgctggtatctggc----ttttccagagactcttacttgcatccagtgatgtaatatgatgtcatatggtttgatggttggcagTTGCTGGGAGATGAAATCGGTAAAGGGGCATATGGCCGAGTGTACAAGGGATTGGATTTGGACAATGGAGATTTTGTGGCGATCAAACAGGTTTCGCTGG
upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatttatcgcgcctcccacctcagatccaggggaattcgtgtttttttgctgc-gaattttggggttatcctactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
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---gggatatgtt----ctcctgctt---gtttttgagattctttggctcaatgtgtcagaatttagcttttctgctagtgtc-ttgactttgaccaattgtatttg---gcagATGCTTGGTGACGAAATTGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGACTTTGTGGCCATTAAACAGGTCTCATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattttggggttatcctactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
ctctcac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggatttatcgcgcctcccacctcagatccaggggaattcgtgtttttttgctgcgaattttggggttatcctactctcactcagtgcgcctgcacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA