Sequence
atgc intronic sequence ATGC exonic sequencegtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctggttttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
--gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacc------tagaagaatgttgtgctggtttt----atcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
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gtgtctggattatttt---tttgtaata-actctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgc--ttgggtacttgaaacgagc------atttagagtacctagaagaatgttgtgctg-gttttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
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--gtatctggatttttttttgtaata-actctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctg--gttttatcatctcatatgcc--cagttacgacattgatgtctat-acaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
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----------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctggttt-tatcatctcatatgcccag-ttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
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----------------------------------------------------------------------------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcc-----tttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
cattgat putative branch site (score: 4)
tgtttttttc putative PPT
tatacaatgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctggttttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG