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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggttttacttgttttggtgtcatacaaaatttattcatattgggtaaagccagatgcatatgagaaataatgctagaaaaaagtgttgtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTAACAGCTGGATTAGTCATTGAAGGTCACACTGGAAATGGCATTCTTGCTC

Basic information

species Vitis vinifera
transcript Vv11s0065g00850.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G07560.1 (Glycine max), 3'ss of exon 3
-gttggttttacttgttttggtgtcatacaaaatttattcatattgggtaaagccagatgcatatgagaaataatgctagaaaaa---agtgttgtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTAACAGCTGGATTAGTCATTGAAGGTCACACTGGAAATGGCATTCTTGCTC
 ||   | | | |       |   || ||  |   || || || ||   ||| || | | |  |    |   ||   | |   ||   | ||||||| || |||||||||||   ||||||||| ||||| || |||||||||||| ||||||| || |||||  |||| |||||||| || ||||| ||  | |||||  |||
tgtaattgtcagtcaggacagaagcaaactgagcatactc-taatg---aaaccctgttcctcaattaactaaaaatttggccaacttaatgttgtgactgcagAGAAGACGCCAAATTGAGGCAATTAACGGAGCATGGGCAATGATTGGTCTCACGGCTGGCCTAGTTATTGAAGGCCAAACTGGGAAAAGTATTCTGACTC
















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|110430063|gb|EC996590.1|EC996590
EST:     GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAG                         AGAAGACGTAGAATTGAGGCGATTAATGGTGCATGGGCAATGCTTGGTCTA
genomic: GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAGgtgaaggaac ... gtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
EST: gi|26265977|gb|CA817040.1|CA817040
EST:     GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAG                         AGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
genomic: GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAGgtgaaggaac ... gtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
EST: gi|26263991|gb|CA815054.1|CA815054
EST:     GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAG                         AGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
genomic: GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAGgtgaaggaac ... gtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
EST: gi|110360710|gb|EC924031.1|EC924031
EST:     GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAG                         AGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
genomic: GTTTAGCTGCCAAACAGATGCAAGAATTTAAAGCAAAAGAGAAACTCAAGgtgaaggaac ... gtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
EST: gi|110421218|gb|EC987509.1|EC987509
EST:     GCAAGAATTTAAAGCAAAAGAGAAACTCAAG                         AGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA
genomic: GCAAGAATTTAAAGCAAAAGAGAAACTCAAGgtgaaggaac ... gtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaaagccagatgcatatgagaaataatgctagaaaaaagtgttgtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTAACAGCTGGATTAGTCATTGAAGGTCACACTGGAAATGGCATTCTTGCTC
               atatgagaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttttacttgttttggtgtcatacaaaatttattcatattgggtaaagccagatgcatatgagaaataatgctagaaaaaagtgttgtggctacagAGAAGACGTAGAATTGAGGCGATTAATGGCGCATGGGCAATGCTTGGTCTAACAGCTGGATTAGTCATTGAAGGTCACACTGGAAATGGCATTCTTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - -tggtgtc
- - - - - - - - - - - - atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - aaagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaa