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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgggtgttgttgaggtctttggagttagaatttttggtactgatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA

Basic information

species Vitis vinifera
transcript Vv08s0007g04310.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 3'ss of exon 4
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttg-ggtgttgttgaggtctttggagttagaatttttggtactgatg-ttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
|    |  |  ||  |||       |  ||||  || |||  | ||  ||    || |  || |||  |  |   || |||||||  |  | |||  ||||| | ||||||||||||||||| |||||  | |||||||| ||||| ||||| || || ||||||||||| ||||||||||| || ||| | || || | ||
ggtgctaggaatctatgatcggactactgctatattccaatcttacccttataatgcttctgcggttct--gccctataattttttttggtcatggctgcagGATATGTTTGAGGAGAAAAGAAGCATACTTGAACCTGCTGGTGCCCTTGCGCTGGCAGGAGCTGAAGCTTACTGCAAATACTATGGCTTGAAAGGGGAAA

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G155323_T01 (Zea mays), 3'ss of exon 4
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttg---acatttgggtgttgttgaggtctttggagttagaatttttggtactgatgt-tgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
  |    | || |  | |         | | | | || | | |     ||||| | |  |  | |  || |||| | |  ||| | |  |  | |||| ||||| | ||||||||||||||||| || ||  | |||||||| ||||| |||||  | ||||| |||||||| ||||||||||| ||   | | || |||| ||
--attcatactcctatcatccttcttcaccaatgctgtatcgtatgtgcattttgcttcttct-atatccttggtgctgaaatatgtctt-ttcatgtgtgcagGATATGTTTGAGGAGAAAAGAAGTATCCTTGAACCTGCTGGTGCCCTTGCATTGGCTGGGGCTGAAGCCTACTGCAAATACTATAACTTGAAAGGAGAAA

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G569855_T01 (Zea mays), 3'ss of exon 4
-----gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgggtgttgttgaggtctttggagttagaatttttggtactgatgt-tgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
       | | |   |||||     |  | |  |||   ||  |  |   ||||| |      | ||  |  |||  | |  ||  |    |  | |||| ||||| | ||||||||||||||||| || ||  | |||||||| ||||| |||||  | ||||| |||||||| ||||||||||| ||   | | || ||||  |
tacattcatactcctttcatctttca--tcaatgctgcattatacat--gcattttg-caccttcgatataattgctgctgaaacatgcctt-ttcatgtgtgcagGATATGTTTGAGGAGAAAAGAAGTATCCTTGAACCTGCCGGTGCCCTTGCATTGGCTGGGGCTGAAGCCTACTGCAAATACTATAACTTGAAAGGAGATA

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G07340.1 (Glycine max), 3'ss of exon 4
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgggtgttgttgaggtctttggagttagaatttttggtactga----tgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
      |||||   |||  ||  |  |  ||   |   |  || | |    | |||  |  |   |  |  | ||     |      | | |    |||||||| | ||||| ||||||||||||| ||| |||||||| |||||||| ||||| || ||||||||||| || ||||||||  || | ||  || ||||   | 
---ctgttgctctgttgttgacattctctctgtctc-taggttcataggctgttgtaatgaaaagcagtaaaattttgtatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGTGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGGTCCAGGGGAAAG

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 4
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacat---ttgggtgttgttgaggtctttggagt-tagaatttttggtactgatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
    |       | ||||  |  |  ||  |    |||||      |    ||  || |   | |  | |||||  | |   |    |   |||  |||||||| | ||||| ||||||||||||| ||| |||||||| ||||| || ||||| || ||||||||||| || ||||||||  || | || ||| ||||   ||
--ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaact--tgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgg-gtgttgttgaggtctttggagtt--agaatttttggtactgatgt-tgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
             || | |  | |  | | || |||    |||| ||   || || | |   | |  |   || ||  |||   |  | ||||  | | | ||| | ||||||||||||||| ||| ||| || ||||| ||||| || ||||| || ||||||||||| || ||||| |||||||| ||| | ||||  |  |
-----------gtatggtacta-tccttgatacgttatcccttgtcagacggtgtttggcatatgcatactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA

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|27585960|gb|CB008655.1|CB008655
EST:     TAGATGGGATAGTTCTTGTAAGCCGTGATGCTATATGTGCCTCAATAAAG                         AACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCC
genomic: TAGATGGGATAGTTCTTGTAAGCCGTGATGCTATATGTGCCTCAATAAAGgtgagtttgc ... gatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCC
EST: gi|30298377|gb|CB975171.1|CB975171
EST:     TAGATGGGATAGTTCTTGTAAGCCGTGATGCTATATGTGCCTCAATAAAG                         AACATGGTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCC
genomic: TAGATGGGATAGTTCTTGTAAGCCGTGATGCTATATGTGCCTCAATAAAGgtgagtttgc ... gatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgggtgttgttgaggtctttggagttagaatttttggtactgatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA
                                         tactgat  putative branch site (score: 2)
                            ttagaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgggtgttgttgaggtctttggagttagaatttttggtactgatgttgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - -tgcttca
- - - - - - - - gaagaag
- - - - - - - - - - - - - - - - - ttgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg