Sequence
atgc intronic sequence ATGC exonic sequence...ctctttcttgctagaatatctgaaaaggcaaggtttttacagctttgtacattaacttcccagttttgaggctacaaaattccttcctccatttgtctagGTTGGCAGCAGGTTTGGAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G34570.1 (Glycine max), 3'ss of exon 6
--ctctttcttgctagaatatctgaaaaggcaaggtttttacagctttgtacattaacttcccagttttgaggctacaaaat----tccttcctccatttgtctagGTTGGCAGCAGGTTTGGAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA
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gatacttctccattcttatatctaaaa---cctgatttagaatatgttgt---ttgactgcataattttgtgggtatctgatactatttttttattctttttctagGTTGGAAGCAGGTTCGGGGAGAGTACTTTTAAACTGGGATCCATACTAACTGATGGTCAAGTTGGCATATTTAAGGATAGATCTGCAGCTGCCATGTCCT
upper sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G16300.3 (Arabidopsis thaliana), 3'ss of exon 5
ctctttcttgctagaatatctgaaaaggcaaggtttttacagctttgtacattaacttcccagttttgaggctacaaaattccttcctccatttgtctagGTTGGCAGCAGGTTTGGAG-AAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA-----------------------
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----------------------------------gtttaggctttggttaattaat-----ggctacaatgttgtaatcgggtttagtatattagaccatgtataaattgttttttcaggaaagCACATTGAAACTGGGATCAATATTAACTGATGGACAAGTGGGAATATTCAAGGACAGATCAGCAGCCGCTATGTCGACATTTGGCGATATACTACCGGCT
upper sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G16300.1 (Arabidopsis thaliana), 3'ss of exon 5
ctctttcttgctagaatatctgaaaaggcaaggtttttacagctttgtacattaacttcccagttttgaggctacaaaattccttcctccatttgtctagGTTGGCAGCAGGTTTG-GAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA------------------
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---------------------------gtaaaggtttag--gctttg---gttaa-ttaatggctacaatgttgtaatcgggtttagtatattagaccatgtataaattgttttttcagGAAAGCACATTGAAACTGGGATCAATATTAACTGATGGACAAGTGGGAATATTCAAGGACAGATCAGCAGCCGCTATGTCGACATTTGGCGATATACTAC
upper sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G16300.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------ctctttcttgctagaatatctgaaa--aggcaaggtttttacagcttt---gtacattaacttcccagttttga---------ggctacaaaattcc--------ttcctccatttgtctagGTTGGCAGCAGGTTTG-GAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA------------------
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gcaagaaactcatggaaggcatttacaaacggcgagcaatctcaaacaagtgatttagaagaaaattccaatttcggcgtggcttttaagtctttcatgcaggtaaaggtttaggctttggttaattaatggctacaatgttgtaatcgggtttagtatattagaccatgtataaattgttttttcagGAAAGCACATTGAAACTGGGATCAATATTAACTGATGGACAAGTGGGAATATTCAAGGACAGATCAGCAGCCGCTATGTCGACATTTGGCGATATACTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacattaacttcccagttttgaggctacaaaattccttcctccatttgtctagGTTGGCAGCAGGTTTGGAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA
cattaac putative branch site (score: 2)
ttccttcctccatttg putative PPT
tacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctttcttgctagaatatctgaaaaggcaaggtttttacagctttgtacattaacttcccagttttgaggctacaaaattccttcctccatttgtctagGTTGGCAGCAGGTTTGGAGAAAGCACGCTGAAACTGGGATCCATATGGACAGATGGACAAGTGGGCAAATTCAAGGACAAATCTGCAGCTGCCATGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - ttcttgc
- - - - - - - - - - -gaaaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cttccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacaaaa