Sequence
atgc intronic sequence ATGC exonic sequence...gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatatatctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 5
gtatttgtgtgctattttaa-atcatttttgctctcagtttttggctgtgtaaaaatgatatatctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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--------gtacttttctcatatggatttggcttgctgtattttctccc------atggtttgtcttgctgca-----actgatataattttgttact-agGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGTGCTCCTGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G083745_T03 (Zea mays), 3'ss of exon 5
gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatatatctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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------gtgagacag---aagtaaaagacgtgtagcttttttgttgttgccgcagttagctggctgtgactaac--tagtatggatttcctgt----cagGTCATTAGGCATTTTGATGGATGCAAAGCAGACTTGGTTGTTTGCGATGGAGCCCCGGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatatatctga--cattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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--ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G31350.1 (Glycine max), 3'ss of exon 1
-gtatttgtgtgctattttaaatcatt-tttgctctcagtttttggctgtgtaaaaatgatatatct-gacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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tttatttgaatttcaactacatgcgttgcttgctttg---ttttggtaagctactttttatttattttgtgaacccccctcttctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G07970.2 (Glycine max), 3'ss of exon 6
gtatttgtgtgctattttaaatcatttttgctctcagtt---tttggctgtgtaaaaatgatat-atctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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--acttgtttgctgga--ggcttctttttcccatcaattaaattatcctcaatgactattgtattatgtttgtgaacccctcttctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTAGTTGTGTGTGATGGTGCGCCTGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 6
------gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatata--tctgacattatccttat---ttatcatcttc--tgttcttc----agGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATG
upper sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
------gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgat--atatctgacattatccttat---ttatcatcttc--tgttcttc----agGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG---------------------------------------
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gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtaaaaatgatatatctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
atctgac putative branch site (score: 3)
tcatcttctgttcttc putative PPT
aaaaatgatatatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatatatctgacattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - -tgtgtgc
- - - - - - - - - aaatcat
- - - - - - - - - - - - - - tgctctc
- - - - - - - - - - - - - - - - - - - - -tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcttc
