Sequence
atgc intronic sequence ATGC exonic sequencegtgtttccttctctgctgatctcttcatttcatttcatttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccctattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g12910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G07880.1 (Glycine max), 3'ss of exon 5
------------------------------------gtgtttccttctctgctgatctcttcatttcatttca-tttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccc-tattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
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gtattgcctgcattatgtcacacactgttattttttggtttattttctctccttaaagaatacttcagtttaaattgaatatctttatctcagc--ttcacccctttcctctcagtctttctctttcgcttggttgtaacaataacttt-tattttaccttgaaaagtagCCCAAATGCGGATTTCTTCCTCTTTCAAGATTCATATCTGAAGTAAATGCTATCAAAAGGAGAATAACCCGATTTGAAATGCACCAAACTCTGAAATTGC
upper sequence: Vv18s0001g12910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G03310.1 (Glycine max), 3'ss of exon 5
------------------------gtgtt-tccttctctgctgatctcttcattt---catttcatttcatctc--ttcagagtatcaatttattttcttctttacaaactt------cttattttactcctctccctattgac--ttcacctttttttctggg-aagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
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gtatgctctccataatgtcatacattattattctttggtacatgtctcacccctctaccattagacaacaacttagtttaaacttcaaatttttaaatcagttatcaaacttgctctcctttactctctcttttgcttgttaacattttaagtggtgttctgaacgagtagCCCAAATGTGGATTTATTCCTCTTTCAAGATTCATATCTGAAGGAACTGCTATCAAAAGGAGGATAACTCGCTTTCAAATGCACCAAGCTCTGAAATTGC
upper sequence: Vv18s0001g12910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G03240.1 (Glycine max), 3'ss of exon 4
---------------------------------------gtgtttccttctctgctgatctcttcatttcatttcatttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccctattg-----acttcacctttttttctgggaagc-agCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
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gtatgctctccataatgtcatacattattattctttggtacatgtcctgcccccct-accattagacaacaacttagtttaaactttaaaattttaaattaattatcaaacttgct--ctcctttactctctctttttcctgttgttaacatttaaagtgttgttctgaacaactagCCCAAATGTGGATTTATTCCTCTTTCAAGATTCATATCTGAAGGAACTGCTATCAAAAGGAGGATAACTCGCTTTCAAATGCACCAAGCTCTGAAATTGC
upper sequence: Vv18s0001g12910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G22100.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtttccttctctgctgatctcttcatttcatttcatttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccctattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
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-------------------------------------------gtgttcgtcattatcttgtgcttacttacttttatgctagccattgaatgcttttagtggctaatat-atgtttgctctgatgaagtagCCCAAATGTGGATTCCTTCCATCTTCAAGTTTCATAGCAGAAGAAAACGTTATTAAGAAGAGTATAACTCGTTTCGAAATGCACCAAGTTCTCAAGCTTA
upper sequence: Vv18s0001g12910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G58936.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtttccttctctgctgatctcttcatttcatttcatttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccctattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
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---------------------------------------gtgtccatgatcattatcttgtcctttctttctttttag--ctcccaatttattctttttttcttcgctgatatatttactttggtgaagtagCCCAAATGTGGATTTCTTTCATCTTCAAGTTTCATAGCGGAAGAAAATGTTATCAAGAAGAGTATAAGTCGCTTCGAAATGTACCAAGTTCTAAAGCTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttcttattttactcctctccctattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
tattgac putative branch site (score: 2)
ttttactcctctccct CT-rich tract
ttattttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttccttctctgctgatctcttcatttcatttcatttcatctcttcagagtatcaatttattttcttctttacaaacttcttattttactcctctccctattgacttcacctttttttctgggaagcagCCCAAATGTGGATTTCTTCCATTTTCAAGATTCATAGCTGAAGGAAATGCTATTAAAAAGAGAGTAACCCGGTTTAGGATGCACCAAATCCTGAAGTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG