Sequence
atgc intronic sequence ATGC exonic sequencegtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttagatcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G043776_T01 (Zea mays), 3'ss of exon 5
gtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttagatcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
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----------gtcagtggctgatttaaccgaagtgtcttcactatgttagcatgggaaatctgtatggctcacactggatgcgc--agGTGCAAGCTGCACGGGATGAGATGCAGTGGGCTGAAGATGGACCTCCACCATTGCTCGTGAAGATTGCACCAGACTTGTCTAAGCAGGATCTTGAGGATA
upper sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G43220.1 (Glycine max), 3'ss of exon 5
--gtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattct---gatattgaatttag---atcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
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gtagaacttgaaactagaatgtgaagctttctccatgtgttttttgtgttgcatacttgggagattgactctagcaaaattttcctttttgtgaagGTTCAAGCTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATAGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
upper sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 5
---gtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttag---atcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
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gtagaacttggaagaatgtaaagctttctccatgagttttttgtgttgcatac-ttgggagcttgactctagcaaaatttgcctttttgtgaagGTTCAAGCTGCTTGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTGGTAAAAATTGCTCCAGATTTGTCAAAAGAAGACCTTGAAGATA
upper sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S291_29V6.1 (Physcomitrella patens), 3'ss of exon 5
----------gt-attttgccgcaggcagaaaattaatg-ttctgttt-atccatttgatcatattctgatattgaatttagatcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
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gtatgcatatgtgaatttcttacattcgaacatctgctgactatatctcagcagcttctacttgacagaacgattaatcctgttcagaggtgcttttgtagGTTCTAGCTGCTCGAGATGAAATGCAGTGGGGAGAGGCTGGGCCACCTCCATTACTGGTGAAAATCTCACCCGATTTATCAAAGCAGGACTTGGCGGACA
upper sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S29_152V6.1 (Physcomitrella patens), 3'ss of exon 6
----------gt-attttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttagatcttttgttt--ccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
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gtactgatacgtgagttttatgtattctgattatctgtctggcggt-atcgaggtaatctccttttgacagtacaactgattcggtagtatactcttacagGTTCTAGCTGCTCGAGATGAAATGCAGTGGGGAGAGGCTGGTCCGCCTCCGTTACTGGTGAAAATTGCTCCTGATTTGTCAAAGCAGGACTTGGCTGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatccatttgatcatattctgatattgaatttagatcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
ttctgat putative branch site (score: 3)
tcttttgtttccatc putative PPT
atattgaatttagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttgccgcaggcagaaaattaatgttctgtttatccatttgatcatattctgatattgaatttagatcttttgtttccatcaagGTTCAAGGTGCTCGTGATGAAATGCAATGGGGTGAGGAGGGCCCACCTCCATTGCTTGTGAAAATTGCTCCAGACTTGTCTAAAGAGGACCTTGAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA