Sequence
atgc intronic sequence ATGC exonic sequence...caagtctctaatttgagatattgtggttcattgttctagaggtgatcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 11
caagtctctaatttgagatattgtggttcattgttctagaggtgat-catgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
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-ataattttaattggaataaatgatgcaaacacatggagtgcaaatgtttgctgtccgcatcctgctgatgcaagttgaagtaatcctttctgcgttgcagGTGCCCGAAAATGTGCAAGAATCGCTTCCGAGGTTGCCATTGCGCAAAGAGTCAGTGTCGCAGCCGGCAGTGTCCATGCTTTGCTGCTGACAGGGAATGT
upper sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G157820_T02 (Zea mays), 3'ss of exon 11
--------caagtctctaatttgagat-attgtggt-tcattgttctagaggtgatcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
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aattagcatgtggcaacaattcaccaccatcctgctgttataattttatggttcaccatgttctttt-----tgtgaaaactt-----atcccttcccttgtgcattcagGTGTCCAAAAATTTGCAAGAATCGTTTTCGAGGATGTCACTGTGCAAAGAGCCAGTGTCGCAGCCGCCAATGTCCATGTTTTGCAGCTGACAGGGAATGC
upper sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G39490.1 (Glycine max), 3'ss of exon 13
caagtctctaatttgagatattgtggttcattgttctagaggtgatcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
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ttacagtttacacagatattttattgcgacttgcctacctgacagccccatgcacccaacatccagtaatgatttctttttttccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGTCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
upper sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 13
caagtctctaatttgagatattgtggtt-cattgttctagaggtgatcatgttatattaatgc-tgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
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tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttccttt--ttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
upper sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G23380.1 (Arabidopsis thaliana), 3'ss of exon 11
caagtctctaatttgagatattgtggttcattgttctagaggtgatcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
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-----------------gtaatgtaatctatgattatccacatctgtatttcttagctttga-atctcattaccaacaaactatattttct---gtgtagTTGCCCAAAGAGCTGCAAGAATAGGTTTAGAGGTTGTCATTGTGCCAAAAGTCAGTGTCGAAGCCGCCAGTGTCCATGCTTTGCTGCAGATCGGGAATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
tattaat putative branch site (score: 2)
tttttttctctctcat putative PPT
tctgaaattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagtctctaatttgagatattgtggttcattgttctagaggtgatcatgttatattaatgctgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT
- - - - - - - - - - ttgtggt
- - - - - - - - - - - - - - - - - - - - - -gatcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctg