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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcatagaatggtaaaagattgttttaactcctactatggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCTCTTCAATAAGCAAAAA

Basic information

species Vitis vinifera
transcript Vv08s0007g03250.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA0084S00210.1 (Glycine max), 3'ss of exon 11
--gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcata-gaatggtaaaagattgttttaactcctactatggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCTCTTCAATAAGCAAAAA
     |  |  |    ||  || |    | |   | ||  |  ||||  || |    |    ||  || ||   |  ||||| | |    ||  | |   |     |     | ||||||||||| ||| |||||||||||||||||  |  ||||||||||||||||||||||  | || ||||||| ||||||||| |||||| | ||||  |   
gtacgtgattttccaagtagtgagtttgtcaggtttatgcaaagcatagttgtttcatggcatggtatttgttttgtgaatgctgatgagtt--tatggttatggttcacactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCAGAAATCATAGAGTATCTAAGAGCAACATACGCTCTTTAGTAAGTGATGC

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G03880.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcatagaatggtaaaagattgttttaac--tcctactatggt-tgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCT-CTTCAATAAGCAAAAA
                                | |  ||  | | |   |  |  ||  |    | | |  |  |  |     | | |     | |   || |  |||| | | | |||  |||||  | ||||||||||||||||||||    |||||||| |||||||||||||| || ||||| ||   ||| |||||| | | | |   |     
-------------------------------gtgagttagagaaatacat--acctagagaaagagaggagaaggtttaaagtatgttgacactgatggtcgtgttatgttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCAGAAATTGTTGAGTATCTCAAGCAAACTTATGCTGCCTAAGTGTTCGTCT-
















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|30253288|gb|CB970839.1|CB970839
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCCCCTTGTTTAGAAGATCCAAACCCTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|27755146|gb|CB035901.1|CB035901
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|110370952|gb|EC934597.1|EC934597
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|32246890|gb|CD712709.1|CD712709
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|110413628|gb|EC979423.1|EC979423
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|27578573|gb|CB001268.1|CB001268
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
EST: gi|110423056|gb|EC989391.1|EC989391
EST:     GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAG                         GCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA
genomic: GTGGCAGCCCAAAACGTCAACTACTGTATCAGAAAGCTAGACATTTTCAGgtatcctcct ... tggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatatggcatagaatggtaaaagattgttttaactcctactatggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCTCTTCAATAAGCAAAAA
                              ttttaac  putative branch site (score: 2)
                    taaaagattgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcatagaatggtaaaagattgttttaactcctactatggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCTCTTCAATAAGCAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA