Sequence
atgc intronic sequence ATGC exonic sequence...attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 4
attcagtccatgtttgttgaatttatagaggtggtttttattt-tcagataattgttcctcaaattcttctgtttatttgtgtacgcctattt---catgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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----agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatgtatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA---
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 4
attcagtccatgtttgttgaatttatagaggtggtttttattt-tcagataattgttcctcaaattcttctgtttatttgtgtacgcctattt---catgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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----agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatgtatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAA---------
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
attcagtccatgtttgttg-aatttatagaggtggtttttattttcag--ataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtcttcagtgatcttaagattcatggtgttcttt---tcctctgatttctgctcagGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 4
attcagtccatgtttgttgaatttatagaggtggtt-tttattttcagataat-tgttcctcaaattcttctgtttatttgtgtacgcctatttca-----tgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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-------ctttgttcatccattttatggtgtaactgaccttttccctaataacatgatgccccattctgtatgatggataacgtatttttttttgggggggcatcagATATTGGACTTCCATCTGGAAAGTCACTTTTCCAACTCCAAGCTGAACGGATCTTGTGCGTTCAGAAGCTGGCTGCTCAATCCAGTGAAA---
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgt------cagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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------tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 5
attcagtccatgtttgttgaatttatagaggtggtttttattt--tcagataattgttcctcaaattcttctgtttatttgtgtacgcc-tatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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--tatgtctaagtaagttgtggt-atttttgtcattttaatgtgctttgagggtaaatcatgaaatatatctttatgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcc-tatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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-tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 4
---attcagtc-catgtttgttgaattt---atagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcctatttc-atgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
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gtgagtaattctcatttttgttatgctctgaataagcttaggttgttgcattgcttgaaggcatgatggttacttaacaaagtagttattgacttatttccatcttagATATCGGATTACCATCAGGGAAATCGCTCTTTCAGATTCAGGCAGAGAGAATCTTGTGTGTTCAAAGACTTGCTGCTCAAGTAGTGAGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
cctatttc CT-rich tract
tgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - -ccatgtt
- - - - - - - - - - - - - - -ggtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcaaa