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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaacaacaagaagatatataaacttgccatttaattctccccatgtctttaattgtaggtttctttcttttttctgctttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCAAACGACGGTACAGAACGACAAGTTGCTAAGCTCATGGAAGAGAATGTTG

Basic information

species Vitis vinifera
transcript Vv07s0141g00220.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G03040.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaatcaacaacaagaagatatataaacttgccatttaattctccccatgtctttaattgtaggtttctttcttttttctgctttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCAAACGACGGTACAGAACGACAAGTTGCTAAGCTCATGGAAGAGAATGTTG------------------
             |||  | | | | |     |||| ||       ||   ||||  |  | | |||  ||    |  ||      | |   | | || |        ||   |||      |||   |||||||||||||||||||| || |||||  | ||||| |||||||| |||||||| || ||||                  
----------gttagactagagagagatacttcattaaaaaaagaacagaactttggtaatggtttttcttgcactgact------tgtggtgtaaaaactttcttcagGATGAGACGCAGGCCG-TGTGGGAGAAATGGTCAAACGATGGGACAGAGAGGCAAGTGGCTAAGCTGATGGAAGAAAACGTTGGAGCAGCGATGCAACTTT

upper sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G02590.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatcaacaacaagaagatatataaacttgccatttaattctccccatgtctttaattgtaggtttctttctttt-ttctgcttt---ttttaa--gGAAGAAGCAAGTGAAGGGGGAAGAAAT---GAACCGGCATGGGAGAAATGGTCAAACGACGGTACAGAACGACAAGTTGCTAAGCTCATGGAAGAGAATGTTG
                     || ||||||   |   |         |   ||||| |  | || || |   |    || |||||    | | ||  ||| ||| |  |||| || ||||| | |    |||| || |||||||||||||| ||||| || || ||||| ||||| ||||| || ||||||||||| |   
--------------------gtaaaaactttttaagaacaaaaagtaaaaactttagtaatggggttttgattcagattttgcttaaaatgtcaatagGATGAAACGGGTGAGGGTGGAAGGACTCCGCAACCAGCGTGGGAGAAATGGTCTAACGATGGGACTGAACGTCAAGTGGCTAAACTGATGGAAGAGAACG---
















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|34550688|gb|CF518906.1|CF518906
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
EST: gi|30303738|gb|CB980532.1|CB980532
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
EST: gi|32459553|gb|CD800727.1|CD800727
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
EST: gi|34549352|gb|CF517584.1|CF517584
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTG
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTG
EST: gi|34549438|gb|CF517670.1|CF517670
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
EST: gi|34550601|gb|CF518819.1|CF518819
EST:     CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG                         GAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA
genomic: CTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAGgtaatcaaca ... tttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctccccatgtctttaattgtaggtttctttcttttttctgctttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCAAACGACGGTACAGAACGACAAGTTGCTAAGCTCATGGAAGAGAATGTTG
              ctttaat  putative branch site (score: 4)
                       taggtttctttctttt  putative PPT
                           tttctttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaacaacaagaagatatataaacttgccatttaattctccccatgtctttaattgtaggtttctttcttttttctgctttttttaagGAAGAAGCAAGTGAAGGGGGAAGAAATGAACCGGCATGGGAGAAATGGTCAAACGACGGTACAGAACGACAAGTTGCTAAGCTCATGGAAGAGAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA