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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaggatagacccaaaactgaattttatttttttgtgtataaattttatttcataggtttgtgattcataaaggtttctaatatcatattttacacttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGCCGTGAAGGGATTTATATTTCACAGTCATCAAGAGCTTTCCGTGACGAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g01790.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 11
gcaggatagacccaaaactgaattttatttttttgtgtataaattttatttcataggtttgtgattcataaaggtttctaatatcatattttacactttt---ccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGCCGTGAAGGGATTTATATTTCACAGTCATCAAGAGCTTTCCGTGACGAAG
      |      ||| ||    ||||||  |   ||| ||||    ||     | ||   || |      ||| |   ||||| ||   || || |||      ||| |||||||||| | ||||||||||||||||||| |||| | ||  ||| ||||||||| |||||| ||  |||    || ||| | |||||||||||||
------ttcctttaaaccttctatttattcatggatgtttaaacaagatagtggaagtac-tgctgacagtaggataacaatataattccttccaatttaatggtagGAATGGAGATCATCAAACCAGGGAAGAAACAATGCTGCATATCGTTACAACCGTGAAGGTATTTATGTTAAACACGGTTCCAGAACATTCCGTGACGAAG
















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|351053644|gb|FQ440153.1|FQ440153
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
EST: gi|56409013|gb|CX017265.1|CX017265
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
EST: gi|56409203|gb|CX017455.1|CX017455
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
EST: gi|56409023|gb|CX017275.1|CX017275
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
EST: gi|56409288|gb|CX017540.1|CX017540
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAGTGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
EST: gi|110364370|gb|EC923996.1|EC923996
EST:     ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAG                         GCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC
genomic: ATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggataga ... acttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataggtttgtgattcataaaggtttctaatatcatattttacacttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGCCGTGAAGGGATTTATATTTCACAGTCATCAAGAGCTTTCCGTGACGAAG
                          ttctaat  putative branch site (score: 2)
                                       ttttacacttttcc  putative PPT
                             taatatcatattttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaggatagacccaaaactgaattttatttttttgtgtataaattttatttcataggtttgtgattcataaaggtttctaatatcatattttacacttttccagGCATGGAGATCACCCAACCAGGGAAGAAACAATGTTGCAAACCGGCACAGCCGTGAAGGGATTTATATTTCACAGTCATCAAGAGCTTTCCGTGACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT