Sequence
atgc intronic sequence ATGC exonic sequencegtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 6
gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctg-tgtgtgttgaggaattattccttttt--------agGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
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gtgagagagtttctttttttatatatttttatgtaacattcttccctgttgtttcatttgatggttattccattcttatgtgtgactgaaagaaaagGTTCCGAGTAAAAATGGTTCATCAACTGAAAAGAAGGATGTCCTATTGGAGGATCATGATCCAATATGGGTTGAGCTCCGGCATGCCCACATAGCAGAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 10
gtaagcctt---ttccaaattttatttatgcttttggatttgatattgtttttcctt-tagctgtgtgtgttgaggaattattccttttt---------agGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
||| | || | | | | || || |||| |||| | || |||| | | | ||| | || || | ||||||||| ||||| || || | || ||||| || ||||| |||||||||||||| ||||||||||||||||| | ||||||||||||||||||
ctaaactttaggccatgggatccaaacagggccttaataatg-tattcttttccattgcctctgtttatactatggattcttttctctgactgaaatgaagGTTCCAACTAAAAATGGGTCGGCAACTGAAAAAAAGGAGGTCCTGTTGGAGGATCATGACCCTGTCTGGCTTGAGCTTAGGCATGCACATATAGCAGAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 10
-------------------gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgt-tgaggaattattccttttt--------agGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
| | | | | | | | | | | | | || | | ||| || || | | | | |||| || | ||||||||||||| | ||| || |||||||| || || | ||||||||||||||||| || ||||||||||| || |||||||||||||| ||
gtgagtacatcagcagcatacagtcttacactgtacctcactagtttaccttattcagttcttactatgtttttga-tgcatgactcttaaaatttatgccaccctcaaacaatagGTTCCAAGTAAGAATGGTTCAGCAAATGAGAAAAAGGAGGTTTTGTTGGAGGATCATGATCCAGTATGGCTTGAGCTGCGGCATGCACATATAGCTCAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 6
gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
|||| ||| | ||| ||| || | | || |||| | | | || ||| | | | |||| ||||||| | ||| | ||||||||| |||||| |||||| || ||||||||||||||||||||||| ||||| || || |||||||| ||||| ||||||
gtaa--cttctacaattttcccttgtcactctgaatttt-tgtgttaactctcttatacataaacacaaaatctactgtatttttaagGTTCCTGGCAAATCCGGTGGTCCAGCAGAGAGAAAAGAGGTTCTTTTGGAGGATCATGATCCTGTATGGCTCGAACTTCGCCATGCTCATATTGCAGAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
gtaagccttttccaaattttatttatgcttttggatt----tgatat-tgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
| || | || | | ||| | | | | | ||| | ||| | | | | | | | | | | | || ||||||| || || || ||||||||||| ||| |||||| || ||||||||||||||||||||| | |||||||| || || ||||||||||| ||||||
----gtgttctataatatctttttccccctctaaactgttgtgacttgtgtccactttcttgttataaatacaaatatactgtat-tcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 10
gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
|||| ||| | ||| ||| || | | || |||| | | | || ||| | | | | |||| ||||||| | ||| | ||||||||| |||||| |||||| || ||||||||||||||||||||| | ||||| || || |||||||| ||||| ||| ||
gtaa--cttctacaattttcccttctcactctgaatttt-tgtgttaactctcttatacataaacacaaaatcttctgtatttttaagGTTCCTGGCAAATCCGGTGGTCCAGCAGAGAGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTCGAACTTCGCCATGCTCATATTGCATAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 10
gtaagccttttccaaattttatttatgcttttggatt----tgatat-tgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
| || | ||| || ||| | | | ||| ||| | |||| | | | || | | | | | || ||||||| || || || ||||||||||| ||| |||||| || || ||||| |||||||||||| | |||||||| || || ||||||||||| ||||||
----gtattctacaatattgttttccccctctaaattgttgtgacttgtgttcactttcttgtcatgaacacaaatctactgtat-tcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTCTTGGACGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
upper sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 10
------gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
||| ||||||| |||| | || || |||| | | | | | | | ||| | || ||||||| ||||||| ||| |||| || | ||||||||| ||||| || || || ||||| ||||||||| | ||||| ||||| || ||||||||||||||||||
gtaagttcaagtcttttccg-----tattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
atttgat putative branch site (score: 5)
ttattccttttt putative PPT
aattattccttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT