Sequence
atgc intronic sequence ATGC exonic sequence...tatgctagagaaaaaaaaatttgaaaagactggaaaagtttttattttttatttttttgagtttatctaacaaatttctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGAGCATTGAAGGGTGGGACACAAGCTACTTCTACGATGAACCAAGTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
tatgctagagaaaaaaaaatttgaaaagactggaaaagtttttattttttatttttttgagt-ttatctaa-----caaattt--ctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGAGCATTGAAGGGTGGGACACAAG-CTACTTCTACGATGAACCAAGTGG
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---gttattaccacaacgttttacatgaaatatttaa-tcttaatcttcgggagactcaaacaccacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCAT----GGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA-
upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 3
---tatgcta-gagaaaaaaaaatttgaaaagactggaaaagtttttattttttatttttttgagtttatctaacaaatttctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGA------GCATTGAAGGGTGGGACACAAGCTACTTCTACGATGAACCAAGTGG
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taacatgtagcaagtctggtcaattcaaacagaaaggaaatacaagttatctgtattttattctctctgaactttggagcttaaattgtgtgtcatgcagGAAGAAGGATGGGTTGTGTGCAGAGCCTTCAAGAAGAAAACCACTGGGCAAACGAAGACTATTAATATTGAAGGATGGGACTCAAGCTACTTCTATGAAG---------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatttttttgagtttatctaacaaatttctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGAGCATTGAAGGGTGGGACACAAGCTACTTCTACGATGAACCAAGTGG
atctaac putative branch site (score: 2)
cttttgc putative PPT
atttttttgagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgctagagaaaaaaaaatttgaaaagactggaaaagtttttattttttatttttttgagtttatctaacaaatttctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGAGCATTGAAGGGTGGGACACAAGCTACTTCTACGATGAACCAAGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
-atgctag
- - - - - aaaaaaa
- - - - - - - - - - - gaaaaga
- - - - - - - - - - - - - - - -ggaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtga