Sequence
atgc intronic sequence ATGC exonic sequence...gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttg--taagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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gctatgctttacg-tcgcgttttaatct-tgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
gcattcttgtgtgatc-ctgttc-taatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttact-ttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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--agttctgtttgaagactgtttacaagttatagttttttctctctc-tgttcaaggtatatgtcatgttttgagattaataataacccactttctgttccagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
-gcattcttgtgtgatcctgttctaatttatatttccttttg-aagaatattgagtttctgggttggaatt-tgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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aatgaggttcccctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttg---ttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 3
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagttt--ctgggttggaatttgtaagttcttactttgaatttgcata----acagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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-----gtgcagtgaactttattctatgcacatagcttggcgctcagtgacacccccaagtagcctatgattt-catcaatttgctgaacattctgatatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttga----atttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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---gacctgaggagtgctactcagacc-acctaaccaactcagctagaggccctttcgcgagtaccagttttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 2
----gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
||| | | || | || || | || | | || | || | | | | || | || || |||| ||||| || || || || ||||||||||| |||||||||||||| |||||| ||| ||| ||||| || ||||| | || || |||||| || ||
agcaaaatttgtacgctatatcggg-tagcgcattacatccagtgcctcacggtcagcctaatatatgtaccatat---tgctgaacatggtcttatcgtgcagGTATGGTGGCGGCCCTTACGAATGAGAGTGCAACCAGCAAATCAGTATACTTTTCACTTTGCACATCGGAAATGATATACATCACTCATCTTCTAGCACC
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgg--gttggaatttgta-agttcttactttgaatttgca---taacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
||| || | | | ||| ||| || | || |||||| | | || |||| | | || |||| | | || |||||||||||||||| ||| |||| |||||||||||||||||||| |||||||||||||| || || ||||| |||||||||||||| || ||||| || ||||
----tctattgagctttgaattccttttctatctcaccat--agtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
-----------gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
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ttgatgttttggactttttgattatttttctgccagttcatgagtcctcttt-------ttatatcgtcaagtcttaaactgtatttatttaatttcaattt----aacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|33403903|gb|CF209530.1|CF209530EST: AACCCATGAAGTTATGGGTGGTTTAAAGAATGCCTATGCCATTGGAGCTG GAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACT
genomic: AACCCATGAAGTTATGGGTGGTTTAAAGAATGCCTATGCCATTGGAGCTGgtaagacagt ... tgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
ttcttac putative branch site (score: 2)
aatttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
gcattct
- - - -tgtgtga
- - - - - - - -cctgttc
- - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - -aagaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgg