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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgtaaccaaccatcatagagtttcaagtacaatatacggattctgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG

Basic information

species Vitis vinifera
transcript Vv06s0004g03140.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 13
--aacgtaaccaaccatcatagagtttc--aagtacaatatacggat--tctgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG
   || | |  || ||| | |   |||   |   | ||   || |||  | |||| | ||  |    |    | |||| |  |  |  |  |  || ||   ||||||||| || ||| | ||||| ||||||||  | || |||||||||||||||||||| ||  ||||||| ||| ||| ||| ||||| || || || ||||
aacacatcataaatcataacaagtttttttagaaataacgaactgataatttgcagt-atgcatcattt---tatatgttccactaactctttctctatg--gcagGCAATCCAGTGTCTTGGTGGAAATGGGTACATAAATGAGTACCCAACTGGTCGTCTCCTGAGAGATGCAAAATTGTTTGAGATTGGTGCCGGTACTAGTG

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 14
aacgtaaccaaccatcataga--gtttcaagtacaatatacggattctgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG
   ||||  || ||   | |   |  ||   || | | |   | | |||   || | |  ||  ||  | |  |   |   |         ||| ||| |||||||| |||||||||||||| ||||| |||||||| ||||| || |||||||||||  |  ||||||||||||| || || ||||| ||||| || ||||
---gtaaataaacaaagttgcttgcatcggttatagt-tgttgttactgttgttcttttattcacattttttagtgcttttacccccccaccaaattttcagGCAATACAATGTTTAGGTGGGAATGGTTATGTGAATGAGTATCCTACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 14
aacgtaaccaaccatcatagagtttcaagtacaatatacggattctgcaattatatagttgtcaaatgtatgatttag-gagtttatattca---attttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG
   ||||  ||     | | |||| |  | |     ||  | |  | |  || |    || |  |    ||  ||||| |  ||||    ||   | ||| ||||| || |||||||||||||| ||||| ||||| || || || || |||||||||||  |  ||||||||||||| || || ||||| ||||| || ||||
---gtaaataa-----acaaagttgctcgcatcggttatagttgttactgttgttcttttattca---cattttttagtgcttttacccccaccaaattttcagGCTATACAATGTTTAGGTGGGAATGGTTATGTAAATGAATATCCCACTGGTCGTCTCTTGAGAGATGCCAAACTCTACGAGATTGGTGCAGGAACTAGTG

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S242_101V6.2 (Physcomitrella patens), 3'ss of exon 16
-------aacgtaaccaaccatcatagagtttcaagtacaatatacggattctgcaattatatagttgtcaa-atg--tatgatttaggagtttatattcaattttg-------cagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG
       |   |  | |   |  |  |  ||||   ||   | | || ||| | || |||  | | | |  | |||  |||  |||  ||||     ||   || |        ||||| ||||||||||| || || || || ||||| || || || ||||||||||| |||||||||||||| || |||||||| ||||| |||||||||||||
gtaactaagtatttctattgagtactgtctttctgatat--tgttcgtatttttcagttagtttgatattgacatggttatattttctgagtactggttttcttataatggtcccagGCCATTCAATGTTTGGGAGGAAACGGATATGTTAATGAATATCCAACTGGTCGGCTTCTTCGAGATGCGAAGCTGTATGAGATTGGAGCAGGGACAAGTG

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|32247850|gb|CD713669.1|CD713669
EST:     CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAG                         GCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT
genomic: CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAGgtgaggtagt ... aattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT
EST: gi|32271070|gb|CD720229.1|CD720229
EST:     CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAG                         GCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT
genomic: CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAGgtgaggtagt ... aattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT
EST: gi|30322661|gb|CD005923.1|CD005923
EST:     CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAG                         GCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT
genomic: CTGGAGTAATACTTTGTGCAGCTGAAAGAGCCACCCAAGTTGCTTTGCAGgtgaggtagt ... aattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG
                                  agtttatattcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgtaaccaaccatcatagagtttcaagtacaatatacggattctgcaattatatagttgtcaaatgtatgatttaggagtttatattcaattttgcagGCAATTCAATGTTTAGGTGGCAATGGGTATGTGAACGAGTACCCAACTGGTCGTCTTCTTCGAGATGCCAAACTGTATGAAATTGGGGCAGGGACAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - -ccaacca
- - - - - - - - - - - - tcaagta
- - - - - - - - - - - - - - - - - - - - - - ctgcaat