Sequence
atgc intronic sequence ATGC exonic sequence...ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4
ttagatcttgctgttgtttaagatg----cattacag-tttttaaaaggtggtta-ttgttgttgtgccctcccccccccccccccccgccctt-ttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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-------ttctttgtgattaaaatgagtccgtcacagactcgtgcaatctcatcagtttatgttaactactaaatgatcattatattcttgttggtttacttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 4
---------ttagatcttgctgttgttta-agatgcattaca-------gtttttaaaaggtggttattgtt-gttgtgccctccccccccccc-ccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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gtgagctcctttcccttcacaattatttgtaactgtatcataagagtatgctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatatattttttgctctgcagGTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgtt--gtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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--tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 1
ttagatcttgctgttgtttaagatgcattacagtttttaaaag--gtggttattgttg-ttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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-gaaaccaaccaataatttttggtt--ttagttttcttaggttttatatcctttgttccttttgtcttatgtaaacttttattaaatgtttgaatttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
---ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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tttttttactttggggtttatttgtctaacttgtggattcttt---gtattcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
---ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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tttttttactttggggattatttgtctaacttgtggattcttt---gtattcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
-ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgtt-gtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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gtgttgtccaacaaatatgtca-atccatt-catttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 4
--ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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tgtattgtctaacaaatacgtg-gatctatt-catttatagtatttttgatttttttttcttgtgtcttgaatgctcattgcttgttttttattcattacagGTATCCAAGGGAAAATGAGGGATTACCAGCTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
-ttagatcttgctgttgtttaagatgcattacagtttttaaa-aggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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gtttgatatattcttcagttgcga-gc-tcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
ttagatcttgctgttgtttaagatgcattacagtt--tttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
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cgtaaccatacatatttttgtga--cctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
tgccctcccccccccc CT-rich tract
tttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - cttgctg
- - - - - - - - - - -gatgcat
- - - - - - - - - - - - - - - - - - - aaaaggt