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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcccaactatttactctcctgtgctttcacttgaacaaatggggaaaactgcaatatatcatatcatatttcagtgctcatattcgatgtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATGGTGTACATGTCATTATGGCGGTAAGGAATGTGGATGCTGGTAGGAATGT

Basic information

species Vitis vinifera
transcript Vv02s0025g03380.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G11410.1 (Arabidopsis thaliana), 3'ss of exon 1
tagcccaactatttactctcctgtgctttcacttgaacaaatggggaaa-actgcaatatatcatatcatatttcagtgctcatattcgatgtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATGGTGTACATGTCATTATGGCGGTAAGGAATGTGGATGCTGGTAGGAATGT
   |  ||  ||| |   |  |  |  ||     ||||| ||   |||  |  | |  | ||  |      |||   ||   || ||  || | ||||||||||| |||||||| |||||   ||||||  |||||||||||||  | | |||||| |||||  | |||||||||||||||   ||| ||||||   | ||
-gactaaaggattaaactttatcaggcttgttaagaacacatcttgaagcaaaggagaagattttgctggtttttgatgtatatgttttatttgatttcagGAGCATCAAGTGGTATTGGGGAAGAGACTACTCGTGTTCTTGCTCTTCGTGGTGTTCATGTTGTAATGGCGGTAAGGAATACAGATTCTGGTAATCAAGT
















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|110369965|gb|EC934139.1|EC934139
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|161715967|gb|FC068756.1|FC068756
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|110373040|gb|EC937247.1|EC937247
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGCTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|71857391|gb|DT006446.1|DT006446
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|110394584|gb|EC959749.1|EC959749
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|71868300|gb|DT017355.1|DT017355
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|110712661|gb|EE087900.1|EE087900
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCGCTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
EST: gi|161706209|gb|FC055419.1|FC055419
EST:     GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAG                         GAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG
genomic: GGAAGTTGCTCAAGGAATTGATGGAAATGGCCTCACTGCTGTTGTTACAGgtctttttcc ... gtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaactgcaatatatcatatcatatttcagtgctcatattcgatgtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATGGTGTACATGTCATTATGGCGGTAAGGAATGTGGATGCTGGTAGGAATGT
         aatatatcatatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcccaactatttactctcctgtgctttcacttgaacaaatggggaaaactgcaatatatcatatcatatttcagtgctcatattcgatgtaatttcagGAGCTTCAAGTGGCATTGGCACAGAGACATCTCGTGTTCTTGCATTGCATGGTGTACATGTCATTATGGCGGTAAGGAATGTGGATGCTGGTAGGAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - ccaacta
- - - - - - - -ctctcct
- - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - -gggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - ctgcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcata