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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgctctaggtcgcctttcaagctccctttatctaatatatccttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA

Basic information

species Vitis vinifera
transcript Vv12s0055g00360.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 9
gtatgctc-taggtcgcctttcaagctccctttatctaatatatccttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA
  ||| |  |  ||      |||   || |  ||        ||  | |    || |  | |            |  ||| |  |    ||  | | |||||  || || |||||||||| |||| | ||||||||| ||||||| ||||||||||| |||| |||||||||| ||||||||||||| ||||| || ||||
-gatgtttatgagtgaatactcactatcacactagaatcaggattgtggccatttaaattgtattttttgtgtgaaatatccatatcttttcacttttcagGCTTTCCTTGAATGGAAGAATGCTAGAAGAGAGGAAGTGTCTGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA

upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G05410.1 (Glycine max), 3'ss of exon 9
----gtatgctctaggtcgcctttcaagctccctttatctaatatatccttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatat--cagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA
     |  |  | |  || || | ||  |    || |   | |||  || | |      || ||||  |         || |||  || |  ||| ||  |  ||||  |||||||||||||||| |||  | ||||||||| |||| || ||||||||||| |||| |||||||||| ||||||||||||| ||||| || ||||
gtttatgggtgcaaactcaccat-cacaccagattcagg-attatggccatttaaa---atgtatcttagtttttgt-ttaatatccatatcttttcactttgcagGCTTTTCTAGAATGGAAGAATGCAAGAAGAGAGGAAGTGTCCGAGTATCAGAAACAGATTGGGGAGCAGTATCTTGCCAATGTTGAGAAGGAATTGGAGA
















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|71883829|gb|DT032884.1|DT032884
EST:     GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAG                         GTATTTCTAGAATGGAAGACTGCTCGAAGAGAGGAACTGTCTGAATATCAG
genomic: GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAGgtgagtttga ... tgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG
EST: gi|71882826|gb|DT031881.1|DT031881
EST:     GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAG                         GTATTTCTAGAATGGAAGACTGCTCGAAGAGAGGAACTGTCTGAATATCAG
genomic: GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAGgtgagtttga ... tgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG
EST: gi|110715632|gb|EE093905.1|EE093905
EST:     GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAG                         GTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG
genomic: GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAGgtgagtttga ... tgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG
EST: gi|71882714|gb|DT031769.1|DT031769
EST:     GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAG                         GTATTTCTAGAATGGAAGACTGCTCGAAGAGAGGAACTGTCTGAATATCAG
genomic: GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAGgtgagtttga ... tgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG
EST: gi|71886910|gb|DT035965.1|DT035965
EST:     GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAG                         GTATTTCTAGAATGGAAGACTGCTCGAAGAGAGGAACTGTCTGAATATCAG
genomic: GCAAACCATTGGAAGAAGATGCAACTGTGGTTGAGCAGCAGAGGGAACAGgtgagtttga ... tgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA
                                 tactcac  putative branch site (score: 1)
                  aaaaaaaaaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctaggtcgcctttcaagctccctttatctaatatatccttgtgtgtttatctatccaaaaaaaaaaatttatactcacaaatttgcatatcagGTATTTCTAGAATGGAAGACTGCTCGGAGAGAGGAACTGTCTGAATATCAGAAACATATTGAGGAGCAGTATATTGCCAATGTTGAAAAGGAGTTAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
gtatgct
- - - - - - - gcctttc
- - - - - - - - - - - - ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaaat