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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTGTTTAGAATGGAGATACACATATCCGCTGCTCGAGGAGGCTGGTTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgttttataatgccttggctcgtattctttgagttaatgctttcccatatatatggtttttgtgtgtgtgtgtgtgtgtgttttggttttatttttatttatttatttttaatcttgttctcttttccttttttatgcatgttttag

Basic information

species Vitis vinifera
transcript Vv01s0011g00550.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00550.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM5G898684_T08 (Zea mays), 5'ss of exon 3
CTCCTGTT-TAGAATGGAGATACACATATCCGCTGCTCGAGGAGGCTGGTTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgttttataatgccttggctcgtattctttgagttaatgctttcccatatatatggtttttgtgtgtgtgtgtgtgtgtgttttggttttatttttatttattt-atttttaatcttgttctcttttccttttttatgcatgttttag
 | ||||| |||||||||||||||| || ||  ||||||||||||| || || ||| | |||||||| ||||| ||||| ||||||||||||||||| |||  |    ||  |||       | | |  | ||  ||  |   |   | |   || |||| |  | |     | |||  |    ||| |  ||| |||  || | |  ||  ||                                    
-TTCTGTTCTAGAATGGAGATACACCTACCCATTGCTCGAGGAGGCCGGATTGGAGGCTTGGGCTGTGGACATCCTTGGGTGGGGCTTCTCTGATTTGGgtacgccccatcctgcaca---ccatgtgatctggtttggttactgtacctg-gtaaggttgtgatttcgtactttgtaggccccttg-taatatctttgcttgtctcgttcgtag-----------------------------------
















Mapped 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|351051568|gb|FQ450120.1|FQ450120
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|351014788|gb|FQ437988.1|FQ437988
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|110361486|gb|EC924960.1|EC924960
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|349808731|gb|FQ406581.1|FQ406581
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|352786080|gb|FQ481875.1|FQ481875
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|351042817|gb|FQ434379.1|FQ434379
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAT
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|351054615|gb|FQ456812.1|FQ456812
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|349829486|gb|FQ420018.1|FQ420018
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
EST: gi|349830592|gb|FQ416890.1|FQ416890
EST:     TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAG                         AAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG
genomic: TTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgtttta ... catgttttagAAAGGCTTCCATCTTGTGACGTGGCAACTAAGCGTGATCACTTTTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTGTTTAGAATGGAGATACACATATCCGCTGCTCGAGGAGGCTGGTTTAGAGACATGGGCTGTTGACATTCTTGGTTGGGGCTTCTCTGATTTAGgtttgttttataatgccttggctcgtattctttgagttaatgctttcccatatatatggtttttgtgtgtgtgtgtgtgtgtgttttggttttatttttatttatttatttttaatcttgttctcttttccttttttatgcatgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT