Sequence
atgc intronic sequence ATGC exonic sequencegtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 2
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtt--tcatcatgatggaggcttcttc-atccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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-------------------------------------------------------gtgtgatttttaagcatttatagttacatctttttaatcactggcttgtagctttgttctgaccaaataattcttatcttgtttgtatttttgacggaaatcttatctt-----------------gtttgtaatt--tgcagGCAGAAGGTATTTTTCGTATAAATGCAGAGAATAGCCAGGAGGAGTTTGTGAGAGATCAGTTAAATAGTGGAATTGTGCCGGATGGCATTGATATTCACT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 2
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatca-tcttccagacttcatcag-actgttgaatat-caatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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-----------------------------------------------------------------------------------------------------------gtatggcttgttagattttaattgattttaaaactat-ttaaattggttactgtttttgttttaatcagtgtctttgtttgtactttgcagGCAGAAGGTATTTTTCGCATAAATGCAGAGAATAGCCAAGAAGAGCTTGTGAGAGACCAATTAAATGGTGGGATCGTGCCAGAGGGTATTGATGTCCACT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 2
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttct-tcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagact---gttgaatatcaatg-cagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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-----------------------------------------------------------------------------------gtgtgtctt-ttatgat-----ctcctatcatcc-tatgattcttagtctgttgccgtcagtgtttggaa-gccttatttctgatcaaataagtgtttccttattttgtactgtcagGCAGAAGGTATCTTCCGTATAAATGCAGAAAATAGCCAGGAAGAGTTTGTGAGAGACCAACTAAATAGTGGAATTGTTCCAGATGGCATTGATGTCCACT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 1
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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---------------------------------------------------------------------------------gtgtgtgttttaggatcttctatgattctttgccctca-gtgtttggaagcctt---atttctgatcaaataagtat-ttccttattttgt---actgt------------cagGCAGAAGGTATCTTCCGAATAAACGCAGAAAATAGCCAGGAAGAATTTGTGAGAGACCAATTAAATAATGGAATTGTTCCTGATGGCGTTGATGTCCACT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 4
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcag----actgttgaat--atcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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-----------------------------------------------------------------------------------------------------caccactctatacaaatttgatcattacttcattttaaatatgactacttgtatgctcctgcttggttaaacagttgaatacttgaattcatccatgcagGCAGAGGGGATTTTCAGAATTAATGCAGATAATAGTCAAGAGGAGTATGTTAGGGATCAATTAAATAGGGGATTGGTCCCAGAAGATGTTGATATACATT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 3
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaat--atcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
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---------------------------------------------------------------------------------------------ttatagatcaccgctctatacaaacgtgataattacttcaatt---tacatatgactacttgtatgctccgg-cttggttaaacagtttaatttattcatgcagGAAGAGGGAATTTTCAGAATTAATGCAGATAATAGTCAAGAGGAGTCTGTTAGGGATCAATTAAATAGGGGATTGGTCCCAGAAGATGTTGATATACATT
upper sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S159_36V6.1 (Physcomitrella patens), 3'ss of exon 3
gtagatcac-ccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
|| | | || |||| | | | |||| || | | | | | | |||||| | | | || | || | ||| | | | | | | || | | || | | | | || | || || || | || | | || ||||| ||||| ||||| || |||||| | ||||||||||| |||||| |||| ||||||||| | || ||| | || ||| | || ||| | ||
gtgtgttgcgtcagaacattggctgaaactaaatttcctgccctgtgcatgg----agcagtttccggctgtagtttgagtaattgtctttccgatgtgctttgataggctttgattaagtaaatataacaccgctc---tttttaaaggacgtctaaattt----atttaatttga-tatttacttctcattcagGCCGAAGGCATTTTCAGGATTAATCCTGAAAACAGCCACGAGGAGCATGTAAGAGAGCAACTCAACCTCGGAATTGTCCCATCGGACATCGATATCCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
aatatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatcacccacaacacaacccccctccctctctcctctccaacgtctagctccaattagctgggataaaagtttggttgaattctgtttcatcatgatggaggcttcttcatccacatgtttcttatttcacttagatctatattgagtttatcatcttccagacttcatcagactgttgaatatcaatgcagGCAGAAGGGATTTTTAGAATTAATGCAGAAAACAGCCAGGAGGAGTATGTGAGAGAGCAATTAAATAGGGGAGTGGTACCAGAAGGAATAGATTTACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA