Sequence
atgc intronic sequence ATGC exonic sequencegtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacattttttt---cctgctcgtct--tctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
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--------------------------------------------gtaacgttaactcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 8
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttct-agGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
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-----------------gtaaatattctggaaacaacataaaactacttctggaagctccatcgt-atgaaatctctagatgctaatattc---------atttttccctgcatctttttatcagAAATGTGAAATACCACGAGCCTGAGTTCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGAC
upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 8
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
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--------------------------------------gtaatgtttacttctacactgttacaacatgaattcaagcgctagatttgatagaggcctgcttgaacctgct-ctattcatatagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGAT
upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
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-------------------atgacaagtaatgtttgt-ttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcct-gcttgaaccttctctattcatat---agGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G133613_T01 (Zea mays), 3'ss of exon 8
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
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---------------gtataaattcctctgaaaaaaaag-cagcgcagcattcgaattgaatcgtcgaaataccag-----ccttcgttttgacatacatgttttctttttcccccacatc-agGAATGCGAAATACCATGAGCCTGAGTTCTGGAAGTTCGGAGAGGACGGGAACAAGTACTTCCGCCACGCCACGGGGCAGATATACGCCATCTCCAAGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
cccttac putative branch site (score: 3)
tctttcctttttttcc CT-rich tract
ttacacattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT