Sequence
atgc intronic sequence ATGC exonic sequence...tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 5
tactactcttcatcagcgtg-gagtaact--ttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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---tgcattgtattgctctataaacaactgattagacaatcttatattatgagataactgatttttttttccttcattttcctgtttccaaattaaatttcagCTTGAATTGGCAGCACCAACTTTGTAAGAATCCACGGCCAAATCCAGATATAAAAACTCTTTTTGTGGATCATTCATGTGGACAACCAAATGGTGCACGG
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 4
---tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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tgtaaatgctcttta--aacaactgattagacaatcttatattatgggata-actgattttttttttcctttttcattttcgtgtttcaaaattaaatttcagCTTGAATTGGCAGCACCAACTTTGTAAGAATCCACGGCCAAATCCAGATATAAAAACTCTTTTTGTGGATCATTCATGTGGACAACTAAATGGTGCACCG
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G22910.1 (Glycine max), 3'ss of exon 4
tactactcttcatcagcgtggagtaacttt----gattcacttcatacaattcagtcacatt-tagtgggttaaaagagaattgattttct-----aatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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----------tatggtcttaggttttccattgaagatactcttttgacaatttgcttaaattatattctattaacaaataattgcttttattttaaaaaataaattacagCCTAAATTGGCAGCATCAACTTTGCAAGAATCCACGGCCAAATCCCGACATAAAAACTCTTTTTGTGGATCACTCATGTGGACAACCAAATGGTGCACGA
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 5
--tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttcta-atacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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tgtggtgctaggttttgcattgaagatactct---tctgtcaatttgattaaattatattctattaacaaagaatacttttattttctttaaaaaaattacagCCTGAATTGGCAGCATCAACTTTGCAAGAATCCACGGCCAAATCCCGACATAAAAACTCTTTTTGTGGATCACTCATGTGGGCAACCAAATGGTGCTCGA
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 8
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgc--agCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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-------------------------------gtgcgtccctgcttttccagctacttctgtgctgatagaagaaatacatttctttttttcttttttcccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTAGCGCGCCGAATGGAGCCCGC
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 4
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaataca-tgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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-------------------------------------------------gttggcacttttttggttcattta----tcccttctaaatgtgctgctgcagTCTGAATTGGCAACATCAATTATGTAAAAATCCTCGGCCCAATCCCGACATCAAAACTTTATTTATCGACCACAGTTGTGGTCCTCCGAACGGAGCGCGT
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 4
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaataca-tgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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-------------------------------------------------gttggcacttttttggttcattta----tcccttctaaatgtgctgctgcagTCTGAATTGGCAACATCAATTATGTAAAAATCCTCGGCCCAATCCCGACATCAAAACTTTATTTATCGATCACAGTTGTGGTCCTCCGAACGGAGCGCGT
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 4
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaa----ttgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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-------------------------------gtgcgtacctgcttttccagctacttctgtgctgatagaagaaatgcatttctttttttctttttttgtccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 4
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctg---cagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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-------------------------------gtgcgtacctgcttttccagctacttctgtgctgatagaaga-aatgcatttctttgtttatttttttccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 4
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
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--------------------gtgcgtccctgcttt--tccagctacttctgt----gctgatagaa-gaaatacatttcgtttttttcttttttcc-cagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
ttctaat putative branch site (score: 2)
aattgattttctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactactcttcatcagcgtggagtaactttgattcacttcatacaattcagtcacatttagtgggttaaaagagaattgattttctaatacatgctgcagCTTGAATTGGCAACATCAACTCTGTAAAAATCCAAGGCCAAATCCAGATATAAAAACTCTTTTTGTAGACCATACATGTGGACAACCAAATGGTGCACGG
- - - - - catcagc
- - - - - - - - - - - - - - - - - - - -catacaa
- - - - - - - - - - - - - - - - - - - - - - - - cagtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagagaa