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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccacttctccctagatctcttgccttgggcttgaactggccctttttctatgtttatatgtttagatgcttgtggcaattgggggattcttctttgttgttggtgtggatgtggttgggttttatctaatctgttaaaatgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGTTCAGGTGCAATTTCATGGACTATAAATGCAAAACATTTTGACCAAGCAC

Basic information

species Vitis vinifera
transcript Vv01s0010g02600.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G19920.1 (Glycine max), 3'ss of exon 8
gtttgtccacttctccctagatctcttgccttgggcttgaactggccctttttctatgtttatatgtttagatgcttgtggcaattgggggattcttctttgttgttggtgtggatgtggttgggttttatctaat-ctg-ttaaaatgattgt-cagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGTTCAGGTGCAATTTCATGGACTATAAATGCAAAACATTTTGACCAAGCAC-
                                                       ||| || | || |||   ||  ||   || |     ||  |    |   |     ||||  || ||  | ||       || ||| ||  | ||| | | ||||||||||||||||| ||||||||||| ||||||| | |  |   |       ||  |     | ||| ||| || || |   | |||   ||   | ||  
-------------------------------------------------------atgcttgtttgattattagcgggtacaaactacaa-atgttggactacagaaaaagtgg--gtagtcagtttgagagagatactgattttattgactttacagATGAATGAAGCAGCAATGGCTGCTCTTGAAGAGAGATTGACCTCTATTGAGACAACTTGTGATACATTGACCATCAA-GAGGACCATCAAGAGGCACCATT
















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|32249424|gb|CD715243.1|CD715243
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|30327377|gb|CD010639.1|CD010639
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|32271592|gb|CD720751.1|CD720751
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|30328045|gb|CD011307.1|CD011307
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGG
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGG
EST: gi|30327866|gb|CD011128.1|CD011128
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|32248801|gb|CD714620.1|CD714620
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|30324225|gb|CD007487.1|CD007487
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
EST: gi|30326365|gb|CD009627.1|CD009627
EST:     GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTG                         ATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT
genomic: GACAGAAAGAGGCTTGTAACAATCTAAGTGGGGCTGATCTTTCTGCACTGgtttgtccac ... tgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttggtgtggatgtggttgggttttatctaatctgttaaaatgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGTTCAGGTGCAATTTCATGGACTATAAATGCAAAACATTTTGACCAAGCAC
                             atctaat  putative branch site (score: 3)
                         ttttatctaatctgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtccacttctccctagatctcttgccttgggcttgaactggccctttttctatgtttatatgtttagatgcttgtggcaattgggggattcttctttgttgttggtgtggatgtggttgggttttatctaatctgttaaaatgattgtcagATGAATGAAGCAGCCATGGCTGCTCTGGAAGAGAAACTCGCAGATTGCAGTTCAGGTGCAATTTCATGGACTATAAATGCAAAACATTTTGACCAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA