Sequence
atgc intronic sequence ATGC exonic sequence...aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
aagaacca--aattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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aagtgctactaacttgtcattactgaaggaaatgtataatctag-cacaacccaaaggatatttaatcatgaagtctctaacttgttgcattttttta-cagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 2
aagaaccaaattaattgcttctaccacttgtttga-tac-ttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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gagagatttttttttcaaaaaaacagagaactcgagcatattagtagtacaaatccttctcaattgctgccactcttctaatgtt-tgtatgat-ctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 2
---aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaat--atgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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gtacatgatctggcaattttttttatctatgggatctgaactaatgcacatattcaataactgcaagttttcagacatcaattatcttgcaagtttt-----cagGTAAAAGAGCATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 2
aagaaccaaattaattgcttc-taccacttgtttgatacttggtcacacaatatgaacccatctat---tttg---actaaactaacatagtgagtaatac----tggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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-----------ttgttgtttggtagcctttattcaaagaatgaaaacataaaaggaacctttttgtcagtttgctctctaactgtaagttttaatcactacaattttttagGTAAAAGGGCATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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---------gttggttggca-tatc-tttctttga-attcag--agaagacttggtgctatctg----aactaagcaagtgtaaatggta-------cagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 1
aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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--------------------gtatttcttctttcatg------catgcattgtgaattttccttttgttgct-------cgt-gtttctgtcgcatgcagGGAAGAGGGCATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCTTGGGAAC
upper sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ25882 (Selaginella moellendorffii), 3'ss of exon 1
aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
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--------------------gtatttcttctttcatgcgtg------cattgtagattttccttttgttgct-------cgt-gtttctgtcgcatgcagGGAAGAGGGCATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCGTGGGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
aactaac putative branch site (score: 1)
atctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- gaaccaa
- - - - - - - - - - ctaccac
- - - - - - - - - - - - - - - - - -tacttgg
- - - - - - - - - - - - - - - - - - - - - tcacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa