Sequence
atgc intronic sequence ATGC exonic sequence...tctttgtaattttctatgtttgtagattttttcctgtgtaaattatatattgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 6
tctttgtaattttctatgtttgtagattttttcctgtgtaaattatat-attgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
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gcaacgttaatga-tagatcaatagatcatgccatggagcttttatgttgtcaattgatgcctatttattatttatcattgatcatgcgtgcatttaacagGAATATGGGCCATACTAAGAAACAATGAAATGCTAACTTGGCCAGAGAAGGTGAAGTTTGCTCTTGGACTTTTGCCAGCAATGGTTGGTGGCCAAGCTTA
upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G473329_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------tctttgtaattttct--atgtttgtagattttttcct-gtgtaaattata-tattgc-tctccgct--tgagttttaat--gcatatttcttgtaaac-atgatt---------------gacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
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gtaagttatacagaacagtggagttattgcaacaggttctctcatttttgctaatatatggacattattaggggttttattagtgacaataataacattacatcgttactgttgagcttaactctgctaattgatgccatactatgattcactattttgcttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACTTGGCCGGAGAAGGTGAAGTTTGCAATCGGACTTCTGCCAGCAATGGTTGGTGGTCAACCTTA
upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------tctttgtaattttct--atgtttgtagattttttcctgtgtaaattata-tattgc-tctccgc--ttgagttt--------taatgcatatt-tcttgtaaa-catgatt--------gacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
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gtaagttatacacaacggtggagttattgcaacaggttctctcatttttgctaatatatggacattattaggggtttattagtgacaataataacattacatcgttaccgttgagcttaactctgctaattgatgtcatactgtgattcactattttgcttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGGCCCGAGAAGGTGAAGTTTGCAATCGGACTTCTGCCAGCAATGGTTGGTGGTCAACCTTA
upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 6
-----tctttgtaattttctatgtttgtagattttttcctgtgtaaattatatattgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
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actgaactccgttgtagcattagcgctgaaatgttctgtggt-tgaatta---atttgtttctggcaaataattaaagt-tgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
ttttaat putative branch site (score: 3)
ttttaatgcatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgtaattttctatgtttgtagattttttcctgtgtaaattatatattgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaca