Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaatatatcttctctggaattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0122g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G109509_T01 (Zea mays), 3'ss of exon 5
gtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaatatatcttctctggaattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
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-------------------------------------------------------aattccagacggaaggcag--attggtcaatgct--------------tgttcactatt-tgcatagaaacatcaacgttttcatccatgttt-----aactattttaatcatttg-tttcagTGTGCCCCACTACACTGAAGAGAATATGCAGGCAGCATGGAATTAATCGTTGGCCATCACGGAAGATTAAGAAAGTTGGGCACTCCCTGAAGAAATTGCA
upper sequence: Vv18s0122g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G01910.1 (Glycine max), 3'ss of exon 5
gtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaata-tatcttctctggaattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
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-------------------------------------------------------------------acattcatgtataatagtgttttacctgttaattttttgtgcatatctatt---agttgtcttcca-ttataaccaaccatcttttaaattaaacaatttc--------cagTTTGTACTACAACTTTGAAAAGGATCTGCCGGCAACATGGGATAAAGCGTTGGCCTTCTCGAAAGATCAAAAAGGTTGGTCACTCTCTACAAAAACTTCA
upper sequence: Vv18s0122g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G02030.1 (Glycine max), 3'ss of exon 3
gtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaata-tatcttctctgg-aattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
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--------------------------------------------------------------------cattcatatatactagtgttttacctgttaatttttctgtgcatatctattagtagtcctccattataaccaaccatcttttaaattaaacatt------------ttccagTTTGTACTACAACTTTGAAAAGGATCTGCCGGCAGCATGGGATAAAGCGTTGGCCTTCTCGAAAGATCAAAAAGGTTGGCCACTCCTTACAAAAACTTCA
upper sequence: Vv18s0122g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G76350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaatatatcttctctggaattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
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---------------------------------------------------------------------------------------------gtaagtaaaacattgacattctcattcttggaatttgaattcatcagagattctgttattgatcttggaattt-----gtttcagTTTGTCCAACGACATTGAAGAGGATATGCAGACAGCATGGGATACAGAGATGGCCTTCAAGAAAAATCAAGAAAGTTGGTCATTCGCTTCAGAAAATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
ttgtaac putative branch site (score: 2)
ccgttctgcttcttc CT-rich tract
taattgattcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgagcctttcgtggctatgataaactgcgattttattcagttattaggaaaattttaattggaaaataataattaatatatcttctctggaattgaactgttcttttctatgctgaattatgttttacttctaattgattctttttgtaaccgttctgcttcttcaatttcagTTTGTCCCACAACCTTGAAAAGGATATGCAGGCAACATGGGATCAAACGTTGGCCTTCTCGGAAAATTAAGAAGGTTGGTCACTCCTTACATAAAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG