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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatccctaaacttatgttgttttttgcggaactgtgggttctacgcaagagggccttgatgttatttgatgtagtgagctgtggactgactttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTCTTGCTGAATCATTGCCTCCTGAACCAAGTGAGCAATCATCAACTCCGCC

Basic information

species Vitis vinifera
transcript Vv10s0003g01150.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G01250.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------gatcccta-aacttatgttgttttttgcggaactgtgggtt-ctacgcaagagggccttgatgtta-tttgatgtagtgagctgtggactgactttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTCTTGCTGAATCATTGCCTCCTGAACCAAGTGAGCAATCATCAACTCCGCC
                                                                        ||   |  |  ||   || ||||||||     |  |  || | |    |   |   |  |  ||   || ||  |        |   ||| |||  |  ||||||| ||||| || ||||| || |||||||||||||||||||||||| || | ||||| || || ||| |||||   ||||||  ||||| ||  ||   
gttcgatctttaatttcaatatagctattctttctttgttttcactttaagattatgatagaaagaataagcataattgtattttgcatttttttttgcaatttttagaattgcaatatgatgcgaattatagattggcttcattcatcttagaattctctggcttgattgcagGTTTTTATGCACCGTGCTCTCACTCTCAAGTATCAAATCATTTAACTGTTTTAGCTGAGTCTTTACCTTCTGAATTGAGTGAGGCATCATTAATCCCTGA
















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|352764554|gb|FQ472911.1|FQ472911
EST:     CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCG                         GTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
genomic: CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCGgttagggttt ... tttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
EST: gi|352773018|gb|FQ470633.1|FQ470633
EST:     CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCG                         GTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
genomic: CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCGgttagggttt ... tttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
EST: gi|352778259|gb|FQ465569.1|FQ465569
EST:     CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCG                         GTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
genomic: CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCGgttagggttt ... tttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
EST: gi|352773901|gb|FQ473033.1|FQ473033
EST:     CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCG                         GTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC
genomic: CTTGAAACTCAACAAACTGGGCATTGATGATTCCCCAATTTCAATCACCGgttagggttt ... tttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagagggccttgatgttatttgatgtagtgagctgtggactgactttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTCTTGCTGAATCATTGCCTCCTGAACCAAGTGAGCAATCATCAACTCCGCC
                                      gactgac  putative branch site (score: 2)
             atgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatccctaaacttatgttgttttttgcggaactgtgggttctacgcaagagggccttgatgttatttgatgtagtgagctgtggactgactttgtgacagGTTTCTATGCCCCATGCTCACATTCTCAAGTATCAAATCATTTAACTCTTCTTGCTGAATCATTGCCTCCTGAACCAAGTGAGCAATCATCAACTCCGCC

- -ccctaaa
- - - - - - - - - - - - - - - - -gtgggtt
- - - - - - - - - - - - - - - - - - - - ctacgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg