Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgcttaatttgtcccgtattgctacccattcatgcggacgagtattctcgttcatctttttcccattccatggccttaatcgaaacctgaatctgttggtggttgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 2
gtaagtgcttaatttgtcccgtattgctacccattcatgcggacgagtattctcgttcatctttttcccattccatggccttaatcgaaacctgaatctgttggtggttgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
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gtaagtgatca------ctcacgct-ctacttttctgcctaagctagc-------ttcatctgttttttcttttctgaatttaactga----------tgatggtgtgagtttaatcagGGGAATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTATGGCTCACTCACCCAGGCGTCCACCATCAGGGTCGGGAGCTACAACGGGGAG
upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 2
gtaagtgcttaatttgtcccgtattgctacccattcatgcggacgagtattctcgttcatctttttcccattccatggccttaatcgaaacctgaatctgttggtggttgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
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----------------------gttagtttcgatttcttagcctctgtcttttggtattattaagaggaaccttgtgttatttatttatgggtcatttttgtattttatgatttctcagGGGCATTTCATGGGCTACAAAGGACAAGATTCAACAAGCCAATTACTTTGGCTCCCTCACCCAAGCCTCAGCTATTCGAGTTGGATCCTTCCAGGGAGAG
upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtg-cttaatt--tgtcccgtattgctacccattcatgcggacga-----------gtattctcgttcatctttttcccattccatggccttaatcgaaacctgaatctgttggtggt-tgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
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gtgagtttcttcgttcttgccctgctttgctccatacttgtttaaaaaaaaaaaaaaactgtttggttggtgagatttgttgatttttttaaaatgatttttaattttgagaagtgggtcatgcattttatcagGGGAATTTCATGGGCAACCAAGGACAAGGTGCAACCAGCCAATTACTTTGGCTCGCTGACTCAGGCATCGACCATCCGAGTTGGGTCCTACAATGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccattccatggccttaatcgaaacctgaatctgttggtggttgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
ccttaat putative branch site (score: 4)
tcgtttc putative PPT
ttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgcttaatttgtcccgtattgctacccattcatgcggacgagtattctcgttcatctttttcccattccatggccttaatcgaaacctgaatctgttggtggttgtcgtttcagGGGGATCTCATGGGCGACCAAGGACAAGGTGCAGCAAGCCAACTACTACGGCTCCCTCACCCAGGCTTCCACCATCAGAGTAGGCAGCTACAACGGGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT