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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATGCATTTCATTTGACATTTGGCTGCGGACTCTTGACATTTTCATTGTTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattgaaatctgtcactatggctatgaaacaactgagagaaactaaacaaagcctaatcccaagtattagggctctgtgaatatgtttttgccact...

Basic information

species Vitis vinifera
transcript Vv08s0007g06550.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06550.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G12100.1 (Arabidopsis thaliana), 5'ss of exon 2
CTGATGCATTTCATTTGACATTTGGCTGCGGACTCTTGACATTTTCATTGTTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattgaaatctgtcactatggctatgaaacaactgagagaaacta-aacaaagcctaatcccaag--tattagggctctgtgaatatgtttttgccact-------------------------------------
|||||||||| |||||||||||||| || || |||||||||||||| || |||||||| ||   |||| |||| ||||||||||| |  ||| | || ||||||| |  || |   |   | |||||   |      | |   |   ||  |   |   |  |||| ||  | | | |    | ||   | ||  |||  | |                                     
CTGATGCATTCCATTTGACATTTGGTTGTGGTCTCTTGACATTTTCTTTATTTGCAATGGCAACTTCAAGGAAGAAGCCTGATCATGCTTACTCATACGGgtgagttacaagtaatttgat-tggctc--agttggttaatccattttatgatctatttttctcccgagactgtaatgtgattatgctcaagtggttgtaatttaggcatccttgtcttctcttttttttgggttcccag
















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|161720919|gb|FC070323.1|FC070323
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|351041060|gb|FQ443836.1|FQ443836
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGT
EST: gi|351017551|gb|FQ435904.1|FQ435904
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|352786912|gb|FQ481287.1|FQ481287
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAAAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|349826952|gb|FQ419043.1|FQ419043
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|351012123|gb|FQ429929.1|FQ429929
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|351026468|gb|FQ428480.1|FQ428480
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
EST: gi|349829079|gb|FQ419611.1|FQ419611
EST:     TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGG                         GTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT
genomic: TTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattga ... attgtatcagGTTCAAAAGGGTAGAAGTTTTGTCTGCTTTCACCAATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGATGCATTTCATTTGACATTTGGCTGCGGACTCTTGACATTTTCATTGTTTGCAATTGCTGTTTCACGGAACAAGCCTGATCAAGTCTACACTTATGGgtgagattgaaatctgtcactatggctatgaaacaactgagagaaactaaacaaagcctaatcccaagtattagggctctgtgaatatgtttttgccact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa