Sequence
atgc intronic sequence ATGC exonic sequencegtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os03g42050.1 (Oryza sativa), 3'ss of exon 18
gtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
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---------gtacagtcttctcactagcttctgtttcatatt----atccctgtgtcattcctg-gtcttagaattgattatattttcattattga---------------------tattttcagAGGGAGACTTTTCCATTTCTTGAAGAATACAGATGTGCCCGCAGTAGAACAACCTTCTACTACATCCTTGGCTGCTTGATTTTCATGGAAGACACCCCAG
upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA06G00520.1 (Glycine max), 3'ss of exon 12
gtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
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------------------------ctccctctctgcactgctgtatttctccacttttcttttttgtagaattagatttcacttatctctgttctaattattttttcactgtaatt--aatctcagAGGGAACATTTTCCATTTTTGGAAGCAAAAAGATGCACTCGCAGCAGAACAACTTTCTATTACACTATTGGCTGGTTGATATTCATGGAAGATAGCCCTG
upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA04G00430.1 (Glycine max), 3'ss of exon 18
gtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
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------------------------tcactctctgcactgctgtatttctccacttttttttttttgtagaatgagattcctcttatccttattctaattattttttcactaaaatt--aatctcagAAGGAACATTTTCCATTTTTGGAAGCAAAAAGATGCACTCGCAGCAGAACGACTTTCTATTACACAATTGGCTGGTTGATATTCATGGAAGATAGCCCTG
upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT5G06120.3 (Arabidopsis thaliana), 3'ss of exon 19
gtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaat-tctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
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------------------------------gtaattcttctccaaggactt--tcttttgtggacatcattgtgcattgtaatttattacgagcaacactctgactatgtgaattgtctaattccagAGGGAGCAATTTCCATTCTTAGAAGAGTATAGATGCTCTCGCAGCAGAACAACGTTTTACTACACTATTGGCTGGTTGATTTTCATGGAGGATAGCTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
ttctaat putative branch site (score: 2)
ttgaaattctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcagctgtgatatatttagtagtttttttttcctcttctttgttctaacctcacttatctgtctttgaaatctttatttcctcttcatttagagattcttttcttgaaattctaatttcagAAGGAGCACTTTCCATTTTTAGAAGAATACAGATGCTCTCGCAGCAGAACAACCTTCTACTACACTATTGGCTGGTTGATTTTCATGGAGGACAGTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA