Sequence
atgc intronic sequence ATGC exonic sequence...gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g14790.1 (Oryza sativa), 3'ss of exon 3
gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaat-ttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
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-cactttgttatgattccattaataaaacagtttctgtcaatcgagaatgaaaaataacggaaatatttaatggttggaataatttcaatctccatattagGTAAGGCGTTCAGATGTTCTTTCTGCCTGGAGTGGTATACGTCCACTGGCTATGGATCCATCGGCAAAAAATACTGAGAGCATTTCCAGAGATCATGTTG
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G28000.1 (Glycine max), 3'ss of exon 3
-gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
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taaacccaaggaaaatgttttgagtgagctgtcactcaatcatgtccttttactattatacc-tctctattttaactttaactaatgctttgaaaatttagGTCCGCCGCACTGATGTTCTTTCTGCCTGGAGTGGCATTCGCCCATTAGCGATGGACCCAACAGCTAAAAATACCGAGAGTATCTCCAGGGATCATGTTG
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G35170.1 (Glycine max), 3'ss of exon 3
----------gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
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caatctacatgtcttttctttttctttttctttgaaaataattaataactgcattttccataccacact--gtttgctgatggggaatgaataatacgg--------tagGTACGCCGTGCGGATGTTCTTTCTGCTTGGAGTGGCATTCGGCCATTAGCAGTGGACCCAACAGCCAAAAATACTGAGAGTATCTCAAGGGATCATGTTG
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G32390.1 (Glycine max), 3'ss of exon 3
-------gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
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tcaatctacatgtcttttttttttcttctttgaaagaattaataattgcattttccataccacact--gtttgctgatggggaatgaataatgcggtgg-----tagGTACGCCGTGTTGATGTTCTTTCTGCTTGGAGTGGCATTCGGCCATTAGCATTGGACCCAACAGCCAAAAATACTGAGAGTATCTCAAGGGATCATGTTG
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G10370.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtatttaatgttag--taactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggaca-atttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
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gtatatccagattcagattaatgaggaataatcaattctatttttgacccaatagctctctaacaattcagttgatga-tgttatgcatcctaaatcttatatagGTTCGACGTACTGATGTTCTTTCGGCTTGGAGTGGGATCCGTCCATTGGCCATGGATCCAACAGCCAAGAGCACAGAGAGTATCTCCAGAGACCACGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
gtctaaa putative branch site (score: 3)
taaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttaatgttagtaactcagtctaggtgtctttttcttttcttttccttctcttatccagtctgcttgtggagtctaaagtatgccgggacaatttagGTACGGCGCACAGATGTTCTCTCTGCTTGGAGTGGCATTCGTCCACTGGCCGTGGATCCAAAGGCGAAAAGCACTGAGAGCATTTCCCGAGATCATGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgcc