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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcccggattctgattccttaatttcttcaaacacatcaatttgagtatcttatttcatcatggagatactgacagttatttctaaatttgactgcaaatctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGGTGTATCCAGCTTCTTGGCTTCTGCACATTTGAAGCATGTGTAGGGATAT

Basic information

species Vitis vinifera
transcript Vv02s0025g02420.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 5
gtatggcccggattctgattccttaatttcttcaaacacatcaatttgagtatcttatttcatcatggagatactgacagttatttctaaatttgactgcaaatctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGGTGTATCCAGCTTCTTGGCTTCTGCACATTTGAAGCATGTGTAGGGATAT
                 || |  |  || | | | || | ||  |||   |  ||  | |  | ||  |    |  ||  || |     |  ||| ||     |  ||| ||||| ||||||| |||||||  ||||||||||||||||| ||||||   || || || |||||||||||||||||  | |||||    ||||| || ||||
---------------gtatgctattcttccattatactcttctctttcc-tccctagtattctgattaaatctcacaccattttgctatatcttgtcttggtgttggaacagTTCTTGGTAGCTCCTTCTGGAGTGAAAGGTGGAAGCATCTCATTCTCTGGTTGCATTCAGCTTCTTGGCTTCTGTGCTTTTGAGAGTTGTGTTGGCATAT

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 5
gtatggcccggattctgattccttaatttcttcaaacacatcaatttgagtatcttatttcatcatggagatactgacagttatttctaaatttgactgcaaatctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGGTGTATCCAGCTTCTTGGCTTCTGCACATTTGAAGCATGTGTAGGGATAT
         | || ||  ||    ||| |  ||       ||      |||||  |  || |   |  | |   |    | | | |||    |||  ||       ||| ||||| ||||||  || || |  ||||||||||||||||| ||||||   || || || |||||||||||||||||  | |||||    ||||| || ||||
---------gtatgctatttttccaatgtactcttctctttcctccctagtattctgattaacatttcacaccatttt-gctgtatcttgtcttggttgtg-----gaacagTTCTTGGTAGTTCCCTCCGGAGTGAAAGGTGGAAGCATCTCATTCTCTGGTTGCATTCAGCTTCTTGGCTTCTGTGCTTTTGAGAGTTGTGTTGGCATAT
















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|33405724|gb|CF211351.1|CF211351
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAA
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAA
EST: gi|33409775|gb|CF215402.1|CF215402
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|110361276|gb|EC924740.1|EC924740
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|77579825|gb|DV218792.1|DV218792
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|33410168|gb|CF215795.1|CF215795
EST:     CTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: CTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|22015506|gb|BQ800540.1|BQ800540
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTATAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|110360915|gb|EC924358.1|EC924358
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCGTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|110413558|gb|EC979348.1|EC979348
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|27585660|gb|CB008355.1|CB008355
EST:     CTGCCTCTCTCCTGCTTCCCACTATAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
genomic: CTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG
EST: gi|161718597|gb|FC068198.1|FC068198
EST:     TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAAT                         TTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAA-GGG
genomic: TTGTGTTTACAATCTCATCTGCCTCTCTCCTGCTTCCCACTGTAATAAATgtatggcccg ... atctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatcatggagatactgacagttatttctaaatttgactgcaaatctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGGTGTATCCAGCTTCTTGGCTTCTGCACATTTGAAGCATGTGTAGGGATAT
                     agttatttctaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcccggattctgattccttaatttcttcaaacacatcaatttgagtatcttatttcatcatggagatactgacagttatttctaaatttgactgcaaatctgaaaagTTCCTGGTAGCACCTTCTGATGTGAAAGGTGGAAGCATTTCATTCAAAGGGTGTATCCAGCTTCTTGGCTTCTGCACATTTGAAGCATGTGTAGGGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC