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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatttaatttctatccaatgctttttccaaccgttattttatgttttcggaatggaatttaatctaactgatcacatttaccaacttggttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATGACTGGGAGGTATCTACGTGATGTGTGGTGATTACTCTTCTATGCAGGCT

Basic information

species Vitis vinifera
transcript Vv11s0052g00880.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 17
--acatttaatttctatccaatgctttttccaaccgttattttatgttttcggaatggaattta-atctaactgatcacatttaccaacttggttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATGACTGGGAGGTATCTACGTGATGTGTGGTGATTACTCTTCTATGCAGGCT
  |  |||  |||    ||||  ||||| |  |   ||  |  || ||||   ||| || | |    ||||   |   | |||   ||  |   | || |||||| ||||| || || |||||||||||||||||||| |||||||| ||||  ||||| || ||| | || ||||| ||||||| |    |  ||||| || 
tgaattttccttttccaccaaaccttttgctgat--ttgatgaat-ttttaaaaattgagtatgtggctaatcaagttcctttgtgaatatcaatcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACTACTGGCAGATATTTGCGCGATGTATGGTGATGATATCTGAATGCAAGCC

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA17G07050.1 (Glycine max), 3'ss of exon 17
acatttaatttctatccaatgctttttccaaccg-ttattttatgttttcggaatggaattta-atctaactgatcacatttaccaacttggttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATGACTGGGAGGTATCTACGTGATGTGTGGTGATTACTCTTCTATGCAGGCT
   ||  ||||| |    |   |||          ||| |  || ||||   ||  |||| |    ||||   |   | |||   ||  |   | || |||||| ||||| || || |||||||||||||||||||| |||||||| ||||  ||||| || ||| | || ||||| ||||||| |    |  ||||| || 
--tttccatttccacaagaccttttgcttgcttacttagtgaattttttaaaaaatgaatctgtggctaatcaagttcctttgtgaatatcaatcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACTACTGGCAGATATTTGCGCGATGTATGGTGATGATATCTGAATGCAAGCC
















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|32267884|gb|CD717043.1|CD717043
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCTCCCAGGCTGAGAGCA
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCA
EST: gi|32270252|gb|CD719411.1|CD719411
EST:     GCATGACAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGAC
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGAC
EST: gi|56409444|gb|CX017696.1|CX017696
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
EST: gi|30326071|gb|CD009333.1|CD009333
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCT
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCT
EST: gi|352774216|gb|FQ474739.1|FQ474739
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
EST: gi|110699884|gb|EE077290.1|EE077290
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATAACATCTTGCAAGAGCAG                         GGGTCTCTAGACAGCTCCCAGGCTGAGAGCATGGTGAAAAATCTGCCAATG
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
EST: gi|30322494|gb|CD005756.1|CD005756
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
EST: gi|32271899|gb|CD721058.1|CD721058
EST:     GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAG                         GGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG
genomic: GCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcat ... ttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcggaatggaatttaatctaactgatcacatttaccaacttggttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATGACTGGGAGGTATCTACGTGATGTGTGGTGATTACTCTTCTATGCAGGCT
           aatttaatctaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatttaatttctatccaatgctttttccaaccgttattttatgttttcggaatggaatttaatctaactgatcacatttaccaacttggttgatttcagGGATCTCTAGACAGCTCCAAGGCTGAGAGCATGGTGAAGAATCTGCAAATGACTGGGAGGTATCTACGTGATGTGTGGTGATTACTCTTCTATGCAGGCT

- - - - - - - -ccaatgc
- - - - - - - - - - - - - -ccaaccg
- - - - - - - - - - - - - - - - - - - - - - - - - -aatggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accaact