Sequence
atgc intronic sequence ATGC exonic sequence...tctgccatcaaacttgagaattttgtacctagatccatgacatagaacacattaaactttgcattgaacatctttctaagccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g38930.1 (Oryza sativa), 3'ss of exon 2
tctgccatcaaacttgagaattttgtac---ctagatccatgacatagaacacattaaactttgcattgaacatcttt--ctaag-----ccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
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----------actttgtgcatcttgtttatactgtccctttcgtctaaaattctctgtaattttcttgggttgtttatacctgaaatgtatttttttcttgagttgccagGGCATGTATCAGCAGCTTCGGCTAGAACCATATGCTGTGCATACTACTTTCCAGTATGCAGGTACTGTGGGAAAGCGTCATAGATTGCGTGAAGCAATGC
upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G09650.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------tctgccatcaa--acttgagaattttgtacctagatcc-atgacatagaacacattaaactttgcattgaacatctttctaagc---cttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
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gtaggatctagttaacaattacaaattccttcttttctgattttatacaatatctactttctgttttcttttacacaattaactgtccaagtgaatctcgcttggaccctgtgatgtagagaaa--caaactgtgtgccagtttttcctaagaatgtacttgcattcatgattgtagGCAATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------tctgccatcaa--acttgagaattttgtacctagatcc-atgacatagaacacattaaactttgcattgaacatctttctaag--ccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
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gtaggatctagttaacaattacaaattccttcttttctgattttatataatatctactattctactttctgttttcttttacacaattaactgtccaagtgaatcttgcgtggaccctgtgatgtagagaaa--caaactgtgttcagtttttcctaagaacatacttgcattcatgattctagGCTATGTATCAGCAACTCAGATTGGAGCCATATGCAGTGCACACAACATTTCAATATGCAGGCACTGAAGGAAAGCGCCACCGACTGCGAGAAGCCATGG
upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 5
---tctgccatcaaacttgagaattttgtacctagatccatgacatagaacacattaaactttgcattgaacatctttctaagccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
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gtacctttcttcatgcttcctgtttttgtgtttt-attatcatcctcttttcttttgtgttcagaaatgacctaacaggtaacttctatt--ttcgatggaagGCTATGTATCAACAACTCAGGCTAGAACCATATGCCGTGCATACAACATTCCAGTATGCAGGTACCGAAGGAAAACGCCACAGGCTTCGAGAGGGGATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacacattaaactttgcattgaacatctttctaagccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
ccttgac putative branch site (score: 4)
attaaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgccatcaaacttgagaattttgtacctagatccatgacatagaacacattaaactttgcattgaacatctttctaagccttgacactatgttggcagTCCATGTATCAACAACTCAGACTGGAGCCATATGCAGTGCATACTACATTCCAGTATGCTGGTACTGACGGAAAGCGTCATAGACTTCGGGAAGCGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - ccatcaa
- - - - - - - - - - - - - - - - - ccatgac
- - - - - - - - - - - - - - - - - - - - - - gaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgacac