Sequence
atgc intronic sequence ATGC exonic sequence...ctaaaagtaaaatttatattcgataaacctactgctcatttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0043g00740.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g05020.1 (Oryza sativa), 3'ss of exon 11
ctaaaagtaaaatttatattcgat---aaacctactgctcatttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaa-ctttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC-
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-tatattta---tttatgtatgatgccaattcttcctgaaatttgagaattcatttgggaacttaaatttaagtttgtccatttttcctttgcttttctttcagGATCCTCTCTGATATGCGAACCCTCTCCGCAGATTGGATGGCCAACACTAGCAAGGGAGATCCAGAAC-ACAACTCGTTAGAAACAGAGGAAATGAGACAA
upper sequence: Vv04s0043g00740.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G170567_T01 (Zea mays), 3'ss of exon 6
ctaaaagtaaaatttatattcg---ataaacctactgctcatttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
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gtaatcgttgaactggttcttgtgtgacaatgtactcctattttgggaatggatttggaaaactaaaaagttttgct---cattttcctttgcattctttcagGATTCTCTCTGATATGCGGACCCTCTCAGCAGATTGGATGGCCAGCACTAGTAAAGCAGACCCAGAGCAGCACTCGCTACACCAAGAAACTGAGGAAATG
upper sequence: Vv04s0043g00740.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G41350.1 (Glycine max), 3'ss of exon 15
ctaaaagtaaaatttat-attcgataaacctactgctcat----ttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
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-----aaaacggttcattgattgaaaagtctgcatcatgtaatactcgtttcttgcttcaagtttttttattgcttatatcaattacccaaatatggattttcagGATTCTTTCAGATATGCGGACCCTTTCAGCTGATTGGATGGCTAATACAAACAAGTCAGAATCTGAGTTACAGTCCTCTCAGCATGGAGGTGAAGAAAGC
upper sequence: Vv04s0043g00740.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA19G43970.1 (Glycine max), 3'ss of exon 14
---ctaaaagtaaaatttatatt-cgataaacctactgctcatttagatttttggttcaaattttcta-attgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
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tcattgattgaaaagtctgcatcatgattcatctaatactcattt-----cttgcttcaagttttttttattgctcatatcaattacccaaatatggattttcagGATTCTTTCAGATATGCGGACCCTTTCAGCTGATTGGATGGCTAATACAAACAAGTCAGAATCTGAGTTACAGTCCTCTCAGCATGGAGGTGAAGAAAGC
upper sequence: Vv04s0043g00740.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G18410.2 (Arabidopsis thaliana), 3'ss of exon 15
ctaaa---agtaaaatttatattcgataaacctactgctcatttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC---
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gtgaattggttttcctttattttctttctgtttcaagtccatgttctcttaaacttaagctttgcatattgttaacttatcatatgta-tggttgcatttcagGATTCTTTCTGATATGCGGACACTTTCAGCTGACTGGATGGCAAATAC---CAGGCCCGAACATGAGATGCCATCTTCACAACATGGAAATGATGAAAGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
ttctaat putative branch site (score: 2)
ctttc putative PPT
ttcaaattttctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaaagtaaaatttatattcgataaacctactgctcatttagatttttggttcaaattttctaattgcttgtttgccgtatgtaattgaaaactttcagGATTCTTTCTGATATGCGGACCCTTTCAGCAGACTGGATGGCAAATACGAGCAGACCTGAATCTGACTTGCAACCTTTACAGCATGGAGGTGAAGAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- aaaagta
- - - - - - - - - - - - aaaccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgcc