Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgaggtttcttcttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 1
gtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgaggtttcttcttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
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--------------------------gtacgtgattgcgagcgagcgttcttgatggtg---gtttggattgggattg--ggttgtgatggtggtggtgatt-cggcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGGCGGCGATCAACGCCGGCGACCGGGTGGACAGCGCGCTCAAGGACATGGCCATCGTGA
upper sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G23380.1 (Glycine max), 3'ss of exon 1
----------------gtaagcttccgttctgggtaatcttgaaatttgc--caacaaac--cgaggtttcttcttttgcgtgattgatctctgtttgatgggtttgat----------tatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
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gtaaattcatttcttcctgggtttttttttcttttcttttccttgtttattacaacaatctacgaggttcttgcccttttggggcttttcaatgtttcaagtgttgagtgttgttccttcgttggttttgtgtgttcagTTGGTGAATAAGGACCCGGAGAGAGCGATTCCGCTGTTCTGGGCAGCCATTAATGCGGGAGATAGAGTGGACAGTGCTTTGAAAGATATGGCTATTGTTA
upper sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G05170.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------------gtaagcttccgttctgggtaatcttgaaa-tttgccaacaaaccgaggtttcttc---ttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
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gtaaatttgccttttgatggattttttcattttgcaactaattttttttagagcaaaaaccttgtaaattgcaaaaaaagaaacaaggtttttgcctcttttttttgcaatttagaaggttttttcccttttcaagtttttttcatgtttcaaatg-ttgagtgttgttctttcgttttgtttttgtgtgtgtgtgt-tcagTTGGTGGATAAGGATCCGGAGAGAGCGATTCCGCTGTTCTGGGCAGCCATTAATGCGGGAGATAGAGTGGACAGTGCTTTGAAAGATATGGCTATTGTTA
upper sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S8_277V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgaggtttcttcttttgcg---tgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
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------gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagccctgaacaatttatgcttga--acaccga--atgaagtttgtttg--cagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
upper sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ08332 (Selaginella moellendorffii), 3'ss of exon 1
gtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgag-gtttcttcttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
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-------------gtaaaagaaagggaccaattccatccgatcgatcgatcgatcggtcgcgcact--gtctc-gcatcgcatctctgagagaacccccttttgg--cagCTGGTGGACAAGGAGCCGGACAAGGCCATCGCGCTCTTCTGGGCGGCGATCAATGCGGGCGACCGCGTGGACAGCGCGCTCAAGGACATGGCGATCGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
cttttgtt CT-rich tract
tttgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgaggtttcttcttttgcgtgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA