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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcatcccatctctcaatgaaagccagagtcatttgcccaaaaatcacagcaggcagtcgaatttcagtgggaatgacttaggaaaaaaattaaatttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTGAGTGGGAAGTACTATCTGGACTGCAATGAGATGGCCCCGAGCGCATATG

Basic information

species Vitis vinifera
transcript Vv08s0040g03400.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g03400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G32920.1 (Glycine max), 3'ss of exon 7
---------------------gtaaatcatcccatctctca-atgaaagccaga-gtcatttgcccaaaaatcacagcaggcagtcgaatt-tcagtgggaatgacttaggaaaaaaattaaatttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTGAGTGGGAAGTACTATCTGGACTGCAATGAGATGGCCCCGAGCGCATATG
                      |  |  || |||    | | ||    || | | || |  |    ||   |   |     ||      || ||| |    ||  | ||   ||||||  ||      |   ||||||||||||| |||||||| ||||| || ||||||||  |||||||||| | ||||||||||| | |||| |||||| |       || ||  || |||
gtattttctttcactccatcattttaggattccactatttatataggtgcaaaatgttacatttgaaagggttcaaaagtccaaatatgttgtcactaatcattgcctaattaaaaaaaaaa------tcatagGGAGCAGCCACGACATGTTATGTTGCTCTCCACCCAAGCGTGAAAGGTGTAACTGGGAAGTACTTTGTGGATTGCAATCAATGCAAACCAAGTTCACATG

upper sequence: Vv08s0040g03400.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G35630.1 (Glycine max), 3'ss of exon 7
--------------gtaaatcatccc---atctctcaatgaaagc-cagagt----catttg------cccaaaaatcacagcaggcagtcg--aatttcagtgggaatgacttaggaaaaaaattaaatttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTGAGTGGGAAGTACTATCTGGACTGCAATGAGATGGCCCCGAGCGCATATG
               |  |||||      ||  | | ||  | |  || | |    ||||||        ||||| ||  |  |    |||   |||  | ||   | | |  ||   | | |  || || | |  | ||||||||||||| ||||| || ||||| || ||||||||  |||||||||| | ||||||||||| | |||| |||||| |       || ||  || | |
gtatttttctttcactccatcattttaggattccactatataggtgcaaaatgttacatttgaaagggttcaaaagtccaaataaattgtcactaatcactgtttaattaatatatatatatatatatatatatcat-agGGAGCAGCCACGACATGCTATGTTGCTCTCCACCCAAGCGTGAAAGGTGTAACTGGGAAGTACTTTGTGGATTGCAATCAATGCAAACCAAGTTCACACG
















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|32250068|gb|CD715887.1|CD715887
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCACAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
EST: gi|254916701|gb|GR905527.1|GR905527
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCACAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
EST: gi|110378703|gb|EC943847.1|EC943847
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCACAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
EST: gi|110417471|gb|EC983528.1|EC983528
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
EST: gi|110425890|gb|EC992285.1|EC992285
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCACAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
EST: gi|110377232|gb|EC942294.1|EC942294
EST:     AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCACAG                         GGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG
genomic: AAATTTTGCAATTGCTCTCGTACATCCTATGGAAGAACGTACCGCAGgtaaatcatc ... ttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcagtcgaatttcagtgggaatgacttaggaaaaaaattaaatttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTGAGTGGGAAGTACTATCTGGACTGCAATGAGATGGCCCCGAGCGCATATG
                                            tttcttttc  CT-rich tract
                         acttaggaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcatcccatctctcaatgaaagccagagtcatttgcccaaaaatcacagcaggcagtcgaatttcagtgggaatgacttaggaaaaaaattaaatttcttttcagGGAGCAGCCACCACATGTTACGTTGCGCTACACCCAAGTATGAAAGGTGTGAGTGGGAAGTACTATCTGGACTGCAATGAGATGGCCCCGAGCGCATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG