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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG

Basic information

species Vitis vinifera
transcript Vv13s0073g00170.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G34000.1 (Glycine max), 3'ss of exon 1
cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattt-----tacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG
  |      ||  || |||      || |   | ||| | |  |  |   ||| ||    ||      ||  | |  ||||     | |  ||||     | ||||||||||| || |||||| | |  ||||||||||||||||| | ||||||||||||||| ||||||||||||||||| ||||| |  |||||||||
ttgggtgcaatggggatttg-----ttttggagggggttgttcgtttttgaattggggatctgaagggttgttaaaagttggatcttttccatttgtgtatgcagATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTTGAAGGCTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAG

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G23810.1 (Glycine max), 3'ss of exon 1
-cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG
  ||   ||| ||| |||| |    |      |          ||| |||  |  |  ||| ||||  |||  ||    |       | ||| |||| ||||| ||||||||||||||||| | ||| |||||||||||||| | |||||||||| |||| ||||  ||||||||||| || || |  |||  ||||
ctgggttttgcttttgcttctttttcaaggtactcacatgtggtgactgctgaatgtgtggttttttttttctttttcttcttctggtttgg-ttttgcagATCAGAACGCATTCTATTCGGAAAGCCCATGAGAATATTGATAGGACTTTGAAGTCTGCAGAGGCCATATTGGCTCACTTTGATCAATATTATCAG

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G33590.1 (Glycine max), 3'ss of exon 1
-cggaacttgatttggcttt-tcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG
   |      ||  || ||| |          | ||  | | |   ||||   ||  |  || || |       ||     |  |  || ||| |||  ||||||||||| || |||||| | |  ||||||||||||||||| | ||||| ||||| ||| ||||||||||||||||| ||||| |  |||||||||
cttgggtgctatggggttttgttttgaggggattgttcgtttttcaagtggggatctgaagggttgttaaaag-ttggatctttttcatttgggttt-gcagATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTCGAAGGTTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAG

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G03540.3 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG
                            ||    |||  || |   ||  |||| ||   ||  ||   ||    |  | || |||   |   | ||    |  ||   | | ||  |  |||||||| || ||| ||||  | | |||||||||||||||||| | |||| | |||||||| || ||||| ||| |||||||||| ||    ||||||
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G03540.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG----
                            ||    |||  || |   ||  |||| ||   ||  ||   ||    |  | || |||   |   | ||    |  ||   | | ||  |  |||||||| || ||| ||||  | | |||||||||||||||||| | |||| | |||||||| || ||||| ||| |||||||||| ||    ||||||    
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGGTTT

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|352773552|gb|FQ472334.1|FQ472334
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|352778158|gb|FQ468820.1|FQ468820
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|110713084|gb|EE088694.1|EE088694
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|110724162|gb|EE099748.1|EE099748
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|352773871|gb|FQ473003.1|FQ473003
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|30297888|gb|CB974682.1|CB974682
EST:     TCTCTGCCCTCG-AACTGCCATGCGTCCCGCTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: TCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|352769773|gb|FQ468701.1|FQ468701
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|37183965|gb|CF603319.1|CF603319
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|352781498|gb|FQ468342.1|FQ468342
EST:     CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: CCTTCGACCACCGTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
EST: gi|30297709|gb|CB974503.1|CB974503
EST:     GTCTCTCTGCCCTCG-AACTGCCATGCGTCCCGCTCAG                         ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG
genomic: GTCTCTCTGCCCTCGAAACTGCCATGCGTCCCACTCAGgtaggtagct ... gattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG
                                  tgctaaa  putative branch site (score: 2)
                      ttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - tggcttt
- - - - - - - - - - ccccctt
- - - - - - - - - - - - - - - tcgtggg
- - - - - - - - - - - - - - - - - - - - - tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - -caatggg