Sequence
atgc intronic sequence ATGC exonic sequence...ccactaaatttgatttttcttggatgatggacaaggttttaatgtgacttttattgacccttttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 10
--ccactaa-atttgatttttcttggatgatggacaaggttttaatgtgac-ttttattgacccttt-tctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
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tacttctaatatttgatttattatagatggttctca-----taaaggtgacaccacattgaccctttctctgtgtacatagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGAGGCCAG
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 11
ccactaaatttgatttttcttggatgatggacaaggtt--ttaatgtgac-ttttattgacccttt-tctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
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----tacttctaatttttgatttataatagatggttttcgtaaagttgacaccacgttgaccctttctctgtgtacatagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATCTCTTGGATGCAAGAAGGTGGCCAG
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 15
--ccactaa-atttgatttttcttggatgatggacaaggttttaatgtgacttttattgacccttt-tctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
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tacttctaatatttgatttataatagatggttctcataaagttgacaccac----attgaccctttctctgtgtacgtagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATCTCTTGGATGCAAGAAGGTGGCCAG
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 9
ccactaaatttgatttttcttggatgatggacaaggttttaatgtgacttt-tattgacccttttctttgcaca-tagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
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-cactgaacctagcaatttgtcgtagatgattctggtaa-aatttaactccatgtcaacttttctgtgtgtaaaatagttttaatatgtcatgtaccactagGTAGCAAAGATGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGTGGCCAG
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 9
ccactaaatttg---atttttcttggatgatggacaaggttttaatgtgacttt-tattgacccttttctttgcaca-tagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
||| || | |||| |||| |||||| | || | ||||| ||| | | ||| || ||| || | | |||||||||| | ||| | ||||||||||||| ||||| | || ||||||||||||||||||||||| || ||||||
-gactgaacctagcaatttgtcttagatgatt--ctag--taaaatgtaactccatgtcaacctttctctatgtaaaatagttttaatatgtcatgtaccactagGTAGCAAAGATGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGTGGCCAG
upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------------------------------------------------------ccactaaatttgatttttcttggatgatg----gacaaggttttaatgtgacttttattgacccttttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
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gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacttttattgacccttttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
atagttttaatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccactaaatttgatttttcttggatgatggacaaggttttaatgtgacttttattgacccttttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
ccactaa
- - - - - - - - ttcttgg
- - - - - - - - - - - - tgatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacata