Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagtagtataagccttcttatctctttaatgaattccatcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g02650.1 (Oryza sativa), 3'ss of exon 5
gtaagtagtagtataagccttcttatct----ctttaatgaa--ttccatcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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gtacttggca-tgttgcttgttctatctgaatccctaatcaaacatccatc-ttgtcttgaaacaagatactccgtataatttatttatgtatcatgtcatcagGTGTTCATATCAACAGAGGACTTCTTGCTCTTGGCAATGTCATCAGTGCTCTCGGTGATGAGAAAAAGAGGAAAGAAGGCGCTCATGTTCCTTACCGGGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 1
----------------------gtaagtagtagtataagccttcttatctcttta-atgaattccatcattctttttgagca--tataaatgatgaaaataag--tttcccccctaattttt--cagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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gtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G15750.1 (Glycine max), 3'ss of exon 5
--------------------------gtaa--gtagtagtataagccttcttatctcttta-atgaattccatcattctttttgagcatataaa-----tgatgaaaataagtttcccccctaatttttca---gGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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gttggtaatgcatgattaacttgaatataatgataatgacatgtatacttttgtttcaaaataccatgtcagaaatactgtttaaataattgaaactgataatgacaaagatttaatgactttgttttataatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTGGGGGATGAAAAAAAGAGGAAGGAGGGTGTGCATGTTCCCTATCGGGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G50240.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtagtagtataagccttcttatctctttaatgaattccatcattc--tttttgagcatataaatgatgaaaataagtttcccccctaattttt-----cagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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-----------------------------gttggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacagGAATTCACATCAATAGGGGACTTCTTGCACTTGGTAATGTTATCAGTGCGCTTGGGGATGAGAAAAGGCGAAAAGAAGGTGCACATGTTCCATACCGTGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S237_18V6.1 (Physcomitrella patens), 3'ss of exon 5
--gtaagt-agtagtataagccttcttatctct-ttaatgaattccatcattctttttgagcatataaatga-tgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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aagcgagccagccccacatgcatatagatcctagttcctgag--ccaagacaaatttcgc-tgtttaattaactgtcggtatgtttggtacgaattatctcagGTATTCACATAAACAGAGGCCTTTTAGCACTTGGAAACGTGATCAGTGCACTAGGTGATGAGAGAAAGCGAAGAGAAGGAGGTCATGTTCCTTATAGAGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S36_179V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagtagtagtataagccttcttatctctttaatgaattccatcattctttttgagcatataaatgatgaaaata----agtttcccccctaatttt--tcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA------------------
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--------------------gagtgtttttgagacgaatgc-gtccttgtattaatgcatg-agattctgaagatgccgtatattgtgggataaccttgttcacgtgtgcacataaatagagGCCTACTAGCACTTGGAAATGTGATCAGTGCACTAGGTGATGAAAAGAAGCGTAAAGAAGGAGGTCACGTTCCTTACCGAGACAGCAAGTTAACACGATT
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ26093 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtagtagtataagccttcttatctctttaatgaattccatcattctttttgagcatataaatgatgaaa-ataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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---------------------------------------------------gttggttttattagtggtttcacgtcaggtttaactttctgtttgcagGTGTTCATATCAATAAGGGACTTTTAGCTCTTGGAAATGTCATCAGTGCTTTGGGAGATGATAAAAAACGTAAAGAAGGAGGGCATGTTCCTTATAGGGA
upper sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ10856 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtagtagtataagccttcttatctctttaatgaattccatcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
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------------------------------------------gttggttttattag--ttgcagaggtttcacgtaaggtttaactttctgtttgcagGTGTTCATATCAATAAGGGACTTTTAGCTCTTGGAAATGTCATCAGTGCTTTGGGAGATGATAAAAAACGTAAAGAAGGAGGGCATGTTCCTTATAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
ccctaat putative branch site (score: 3)
tttcccccctaatttt CT-rich tract
atataaatgatgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagtagtataagccttcttatctctttaatgaattccatcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG