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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccctttgcccatttaatcaatgaatggataatttggtcgtttatgtcttttacacatttttttttcttttttctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGTTTTTGTCTTGGTCACACAGA

Basic information

species Vitis vinifera
transcript Vv07s0151g00790.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0151g00790.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G03110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtactccctttgcccatttaatcaatgaatggataatttggt-cgtttatgtcttttacacatttttttttc-ttttttctgctg--acagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGTTTTTGTCTTGGTCACACAGA
        |  ||   | ||||| |  |||| | ||| |  | | ||| |  ||   |    | || |  |  || | | |||    ||||||  | || || |||||||||||  |||| || |||||||| || ||||||||||||||||| ||  ||||
-------gtaagctagtctaatccactaatgcacaatgtcatacctttcttgctcagattggtcttatagtgattctgtttgccatcacagGTGACTGTTTTTCCCAAGAAGCCTCTAGAAGGGGCTCATGAAATACAGAGTTTTTGTCTTGGACATTCAGA
















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|349827480|gb|FQ422348.1|FQ422348
EST:     CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGT                         GTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
genomic: CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGTgtactccctt ... ctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
EST: gi|351025295|gb|FQ434308.1|FQ434308
EST:     CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGT                         GTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGGGATCCAGAGT
genomic: CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGTgtactccctt ... ctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
EST: gi|349826552|gb|FQ418643.1|FQ418643
EST:     CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGT                         GTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
genomic: CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGTgtactccctt ... ctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
EST: gi|122690606|gb|EC954888.1|EC954888
EST:     CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGT                         GTTTCTGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT
genomic: CACTGGATGGGCGATTCATTATTAGTGCTGATCGGGATTTTAAAATTCGTgtactccctt ... ctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatttggtcgtttatgtcttttacacatttttttttcttttttctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGTTTTTGTCTTGGTCACACAGA
            tttatgtcttttacac  CT-rich tract
                  tcttttacacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactccctttgcccatttaatcaatgaatggataatttggtcgtttatgtcttttacacatttttttttcttttttctgctgacagGTTTCCGTGTTCCCCAAGAAGCCCTTAGATGGAGCTCATGAGATCCAGAGTTTTTGTCTTGGTCACACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC