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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtttgttaagtttgatgctgagaatttaaattcatgtgatattgtcacattttttatacatgctattgagatatcttttggtgtttttgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGTGGAAATGGGTCTATCACACAAAATTTGCGAGTTACTAACAGCCTACATG

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 16
gaagtttgttaagttt--gatgctgagaatttaaattc-atgtgatattgtcacattttttatacatgctattgagatatcttttggtgtttttgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGTGGAAATGGGTCTATCACACAAAATTTGCGAGTTACTAACAGCCTACATG
 |  | | | || |||  |||||| |  ||||| |||         || || |  || ||||| |||    ||   |  |  |||| | ||||| | |  ||||||||||||||| |||||||| |||| || ||||| || || ||||| |||||||| |||||  ||||||||||| ||  ||||||||| |||| ||| |
-agttgtttcaactttcggatgctaaatatttacattttgcaaatcatggttatcttatttat-catctactttttacttactttgat-tttttaattttcagTTTCTTCAGTTGAACTTAGATCCAGCTAGCGGCAATACTCTCCCTGCTAGTGGAAAGGGGTCCGTCACACAAAATATGAAAGTTACTAATAGCCAACACG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 16
--gaagtt-tgttaagtttgatgctgagaatttaaattcatgtga--tattgtcacattttttatacatgctattgagatatcttttggtgtttttgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGTGGAAATGGGTCTATCACACAAAATTTGCGAGTTACTAACAGCCTACATG-----
  |  ||| |  |  ||    || ||  | || ||| || | |||  |  | |   |  ||  || |||    |    | || |||||    |||  | |  |||||||||||||||||||||||| |||| ||  |||| || ||||| ||||      ||||||| || || |||| ||||  | ||||||| |||| |||||     
gagccgttctactgggtgctttgttggaatttcaaaatcttttgaactgctttgttaccttccat-catctagtacttacatattttg----tttcaattttcagTTTCTTCAGTTGCACTTAGATCCAGCTAGCAGCAATACTCTTCCCGCAA------ATGGGTCCATAACCCAAAGTTTGAAAATTACTAATAGCCAACATGGGAAG
















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|30126008|gb|CB911347.1|CB911347
EST:     TGTCACCTAATATCTTTACAGATTTTATTTTCCAGGCAGCAGTCCCGAAG                         TTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGT
genomic: TGTCACCTAATATCTTTACAGATTTTATTTTCCAGGCAGCAGTCCCAAAGgtaacactag ... tgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGT
EST: gi|156723711|gb|EV228503.1|EV228503
EST:     TGTCACCTAATATCTTTACAGATTTTATTTTCCAGGCAGCAGTCCCAAAG                         TTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGT
genomic: TGTCACCTAATATCTTTACAGATTTTATTTTCCAGGCAGCAGTCCCAAAGgtaacactag ... tgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcacattttttatacatgctattgagatatcttttggtgtttttgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGTGGAAATGGGTCTATCACACAAAATTTGCGAGTTACTAACAGCCTACATG
                                       tgttttt  CT-rich tract
      attttttatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtttgttaagtttgatgctgagaatttaaattcatgtgatattgtcacattttttatacatgctattgagatatcttttggtgtttttgagtcacagTTTCTTCAGTTGCACTTAGATTCAGCCAGTGGCAACACACTTCCTGCAAGTGGAAATGGGTCTATCACACAAAATTTGCGAGTTACTAACAGCCTACATG

- - - - - - - - gatgctg
- - - - - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt