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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagccactatttgtattctgaacttctagccttgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06060.1 (Glycine max), 3'ss of exon 5
aagccactatttgtattctg-aacttctagccttgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttg-tagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG
  ||  || |   || |  |  |    |  | || |       ||||    || |  | ||| || |  || ||     || |  ||||||||||||  |||||| |||| ||||| || ||| | ||||||||||||||| ||||||| |||||||||
ctgcttctgtcattaattggcgaagcattacttttatactttctaaaatgtttgt--taatgtcttttcaatttgatgattttgtcatgcttcttttaatagGGCATTCGTGTTGGTCTTAACCTTGCACTGGCCATTGCTCTGCACAATATCCCAGAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14090.1 (Glycine max), 3'ss of exon 4
aagccactatttgtattctgaacttctagcct---tgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttg-tagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG
   |  |||||  || |  |    | |  | |   |       ||||    | || | || ||||   ||||  |  | ||  ||  ||||||||||||  |||||| |||| ||||| || ||| | || |||||||||||| ||||||| |||||||||
---cttctattgctaattggcgtatattacttgtatactatctaatagtatatttttgttaatgcacttcaatttgatgatc-gtgtcatgcttcttttaatagGGCATTCGTGTTGGTCTTAACCTTGCCCTGGCCATTGCTCTGCACAATATCCCAGAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ16604 (Selaginella moellendorffii), 3'ss of exon 6
aagccactatttgtattctgaacttctagccttgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG
                                |  | |||| |  | | |||||    |   ||  |||  ||     ||| |||||        |  ||||| |||| |||||  ||| ||| || ||||||||||||||||||||||||||||||
-------------------------------gtatgaaacact--accgcttattgaaaaaacttccaaccttacgcgttgctacat--------ttcagGGCATTCGAGTTGGTATAAGCTTAGCCCTGGCCATTGCTTTGCACAACATCCCAGAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ32545 (Selaginella moellendorffii), 3'ss of exon 6
aagccactatttgtattctgaacttctagccttgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG
                                |  | |||| |  | | |||||    |   ||  |||  ||     ||| |||||        |  ||||| |||| |||||  ||| ||| || ||||||||||||||||||||||||||||||
-------------------------------gtatgaaacact--accgcttattgaaaaaacttccaaccttacgcgttgctacat--------ttcagGGCATTCGAGTTGGCATAAGCTTAGCCCTGGCCATTGCTTTGCACAACATCCCAGAG

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|30251805|gb|CB969538.1|CB969538
EST:     TGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCANTGGCCATTGCTTTGCACAACATC
genomic: TGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     GAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTCGGACTATCCTTGGNTCTNGCCATTGCTTTGCACAACATC
genomic: GAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110693804|gb|EE070356.1|EE070356
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110689440|gb|EE065664.1|EE065664
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110698572|gb|EE076222.1|EE076222
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG
        tattgat  putative branch site (score: 3)
                                         tgcttctttt  putative PPT
                      aaaattttcatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagccactatttgtattctgaacttctagccttgaggaacaataaatcacttatattgatgcctctcaaaattttcatttgttacatgcttcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATCCCAGAG

- gccacta
- - - - - - - - - - - - - -agccttg
- - - - - - - - - - - - - - - - - -ggaacaa
- - - - - - - - - - - - - - - - - - - - - -aaatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct