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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaaataggtttgctgatttttggttcctgatattgttccactcatcagaaatctgtagtgtttgactctgagaactatttcccctcttttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG

Basic information

species Vitis vinifera
transcript Vv02s0025g01410.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 16
--------------------------------------------------ggtaaataggtttgctgatttttggttcctgatattgttccactcatcagaaatctgtagtgtttgactc-tgagaactatttcccctcttttaa----ttgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG
                                                   ||  ||    | ||  ||          |||| || ||   || ||     |  |||  || |  |       ||| |   | |  ||||||      ||  |||||||||| || || ||||||||||||||||| ||||||||||| |  || |||||  || | |  || ||  | ||||||  ||  ||    ||   ||
gtatgtaatggacaacattttaatttttctggtcttttcaaattttctgtagtctatgaaat-gcgaataaaaccagattgattttcttaggcttatgtcctagttgttctgctgaaggaacatgaattggcttcaatctttttgaattttttagATATGGATATATGGGAACAGCTTTGAGTCCTTTCTTGTTGCTGTGGTCAATCCCAACAAGGAGGTTCTCGAGAGTTGGGCTGCAGCAAATGGAATAAGTG

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 16
ggtaaataggtttgctgattt--ttggttcctgatattgttcca--ctcatcagaaatctgtagtgtttgactctgagaactatttcccctcttttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG
  | |  | ||     | |||  |    | |  | || |   ||  ||  | |  || ||  | | | |||  |||| ||   | | |  ||| |  ||| ||||||||| |||| || ||||| || ||| |||||||||||||||||| |||||||| | |||||||||||||||  |||||  |||| ||    || ||  
-atgatgatgtcaaaaggtttagtccagtgcaaaaatagaaacaaacttttgaataagcttcactttatgag-ctgaaaatgttctgcattctct--atttcagATATGGGTTTATGGAAACAGTTTCGAGGCCTTCCTTGTTGCTGTTGTTAACCCCAGTAAGCAAGCACTTGAACATTGGGCACAAGAAAATGGCATATCCA

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA01G43470.4 (Glycine max), 3'ss of exon 16
ggtaaataggtttgctgattt--ttggttcctgatattgttcca--ctcatcagaaatctgtagtgtttgactctgagaactatttcccctcttttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG
  | |  | ||     | |||  |    | |  | || |   ||  ||  | |  ||  |  | | | |||  |||| ||   | | |  ||| |  ||| ||||||||| |||| || ||||| |||||| |||||||||| ||||||| |||||||| | |||||||||||||||  |||||  |||| ||   ||| ||  
-atgatgatgtcaaaaggtttagtccagtgcaaaaatagaaacaaacttttaaataagtttcactttatgag-ctgacaatgttctgcgttctct--atttcagATATGGGTTTATGGAAACAGTTTTGAGGCCTTCCTTGTGGCTGTTGTTAACCCCAGTAAGCAAGCACTTGAACATTGGGCCCAAGAAAATGGTATATCCA

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|30125801|gb|CB911140.1|CB911140
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|110375957|gb|EC940989.1|EC940989
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|27580341|gb|CB003036.1|CB003036
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|349816864|gb|FQ399732.1|FQ399732
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCCTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|352781554|gb|FQ468398.1|FQ468398
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|351053855|gb|FQ441621.1|FQ441621
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|32245315|gb|CD711134.1|CD711134
EST:     AAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: AAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|27755362|gb|CB036117.1|CB036117
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagaaatctgtagtgtttgactctgagaactatttcccctcttttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG
                                           ttttaat  putative branch site (score: 3)
                               ctatttcccctctttt  CT-rich tract
                                         tcttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaaataggtttgctgatttttggttcctgatattgttccactcatcagaaatctgtagtgtttgactctgagaactatttcccctcttttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAACCCCAATCAGCAAGCACTTGAACGGTGGGCTAAAGAGAACAATATTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- -aaatagg
- - - - - - tgctgat
- - - - - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - - - -ccactca
- - - - - - - - - - - - - - - - - - - - - - - - agaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gactctg