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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaatcaatatttatatagtcctgttaatttaatcatgtatctgttcattgctcagccgcattttctattcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT

Basic information

species Vitis vinifera
transcript Vv12s0028g01120.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 8
gtattaatcaatattta-tatagtcctgttaatttaatcatgtatctgttcattgctcagccgcattttct---attcata-----------cagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT
||||  || | | |  | | | ||  ||  ||| |     |    |  |   ||||| | |   ||||  |   ||| |||           |||||| ||||||||||| ||||  ||||||| ||| ||||| ||||| ||| |||||| | ||||||||||||| || || ||||||||||| ||  |||| 
gtatgtattagtttaaagtttggttttggaaatctg--tgtcccccattgtgttgcttaactaaatttattggcattgataatacctcttctcagGGTAACAAAAATAGTTAGGCAATATAATGAAGTAAAGGTGACAGTGGAAAATGGGAAAACATTTGTTGCAGACGCCGCTATTGTTGCTGTACCTCTTGGG

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G03610.1 (Glycine max), 3'ss of exon 8
gtattaatcaatattta-tatagtcctgttaatttaatcatgtatctgttcattgctcagccgcattt------tctattcatac--------agGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT
||||  || | | |  | | | ||  ||  ||| |   | |    |  |   ||||| | |   ||||       ||  | ||||        ||||| ||||||||||| ||||  ||||||| ||| |||||  |||| ||| |||||| | ||||||||||||| ||||| ||||||||||| ||  |||| 
gtatatattagtttaaagtttggttttggaaatctg--cgtcccccgttgtgttgcttaactaaatttaatggcactgataatacctcttctcagGGTAACAAAAATAGTTAGGCAATATAATGAAGTAAAGGTGGCAGTGGAAAATGGGAAAACATTTGTTGCAGACGCTGCTATTGTTGCTGTACCTCTTGGG

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 8
gtattaatcaatatttatatagtcctgttaatttaatcatgta-tctgttcattgctcagcc------gcatt----ttctattcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT
||| | || | |  ||  || ||  | | ||  |    ||||| | | || | |  | |         || ||    |||  ||  | |||||| |||||| |||| ||||| ||||||||||| |||||||| || ||| |||||| | | ||| |||| ||||||||  || ||||||||||  |||| 
gtacttattatt--ttgaattgttgtttcaaaatttgtatgtactgttttgagtagttaaatttacgggctttggaattcccttttttcagGGTCACAAAAGTAGTTAGGCGATATAATGGAGTAAAGGTAACTGTGGAAAATGGGAAAACGTTTTTTGCTGATGCTGCTGTTATTGCTGTCCCACTTGGG

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 8
-----------gtattaatcaatatttatatagtcctgttaatttaatcatgtatctg---ttcattgctcagccgcatt-ttctattcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT
            | | ||  |  |||| || | |  | |  | |   || | ||  |    ||  || ||     |  |  | |      | |||||| |||||| |||| ||||| ||||||||||| ||||||||||| |||  ||||| | | ||| |||| ||||||||  || ||||||||||  |||| 
ggtagatattattttgaactatcatttttagaattttatgtactatttcgtttagttaaatttacttactggcttgggtaatgcccccttttcaGGGTCACAAAAGTAGTTAGGCGATATAATGGAGTAAAGGTAACAGTGGAAAGTGGGAAAACGTTTTTTGCTGATGCTGCTGTTATTGCTGTCCCACTTGG-

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|110718353|gb|EE095090.1|EE095090
EST:     CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAG                         GGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
genomic: CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAGgtattaatca ... attcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
EST: gi|110718889|gb|EE096234.1|EE096234
EST:     CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAG                         GGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
genomic: CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAGgtattaatca ... attcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
EST: gi|110377101|gb|EC942162.1|EC942162
EST:     CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAG                         GGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
genomic: CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAGgtattaatca ... attcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
EST: gi|110698188|gb|EE075460.1|EE075460
EST:     CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAG                         GGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
genomic: CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAGgtattaatca ... attcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
EST: gi|110388093|gb|EC952810.1|EC952810
EST:     CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAG                         GGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA
genomic: CCTGTTATAAACACCCTCGCAAAAGGTCTCGACATCCACTTGAACCACAGgtattaatca ... attcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatttaatcatgtatctgttcattgctcagccgcattttctattcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT
                                       ttttctattc  CT-rich tract
     atttaatcatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaatcaatatttatatagtcctgttaatttaatcatgtatctgttcattgctcagccgcattttctattcatacagGGTTACAAAAATAGTAAGGCGTTATAATGGAGTCAAGGTAACAGTAGAAGATGGGAGATCATTTGTTGCAGATGCTGCCATTGTTGCTGTCCCCATTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC