Sequence
atgc intronic sequence ATGC exonic sequencegtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 5
--------gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgac--aaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
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gtacgcctgcttcctcagctcatacgattgctacatttttt--atgcttggtattgcaccttgatttcaattgttttattcttgatcaaaatctttcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTAT
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 6
--gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
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gtatgttcctactagttctcaaatcg---ctgcactgaccaatgttttattcttcttcagctaactctgtagtttctga--acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCAT
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g64670.3 (Oryza sativa), 3'ss of exon 6
--gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT------------------
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gtatgttcctactagttctcaaatcg---ctgcactgaccaatgttttattcttcttcagctaactctgtagtttctga--acttattcagACAAGAAGAATGAAAACAAGGAGGTCGCCGTGAATGAGGTACTGCCTGTGACCGCTGCTCGGGATGCCATCCAGTATTCCATGTAAGTGATGAACTGTCC
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 7
gtat---ccttttcatctt----tcagttcaacctttcatgaaaatttgttaaggggatga-acaatagac---aaattttttcttgacaaac--aatt--cagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
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gtacgcaccatttcgtctccaaatctgtctgattttttttttctttctatgatcgtagcgctacggttgctttgaaatccatttcacatgtatttaatttgcagACAAGAAGAACGAGAACAAGGAGGTTGCTGTGAACGATTTCTTGCCACCAACTACTTCCCTGGAGGCCATTCAACACTCAAT
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaatt--ttttcttgac--aaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
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---------gtatccttaa----aacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
tttcttgac putative branch site
aatagacaaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaattttttcttgacaaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG