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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttcactccttttatcaatgtctaagaaataaattcccttgcattttgccagtcacatgcatcatttaattgatagtttgcttcgaaatgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGA

Basic information

species Vitis vinifera
transcript Vv08s0007g02170.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G856436_T02 (Zea mays), 3'ss of exon 2
----gtttt-cactcc--ttttatcaatgtctaagaaataaattcccttgcattttgccagtcac---atgcatcatttaattgatagtttgcttcgaaatgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGA
    || || |  | |    || || |    ||||  |||  |      | |||||| ||| ||    ||| |||||| || | || || || |     || |    |||||  ||||| ||    ||||  || ||||||||  |||||||||| |||||||| ||||||  ||| || ||||||||||| ||||| ||||| ||||||
tttggtattacggtgcagcgttttccagagataagtcatatttcttacagtattttgtcagacagcagatgtatcatt-aactcat-gtctgtt-----atac---ccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGA

upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G18040.1 (Glycine max), 3'ss of exon 1
-gttttcactcctttt--atcaatgtctaagaaataaattcccttgcattttgccagtcacatgcatcatttaattgatagtttgcttcgaaatgc-atgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGA
   | | | | ||  |  || ||  |  || |  |||  || ||   |||  |  |   | ||| ||  || || | |||  ||| |     |||  ||| ||||||||||||||| || || ||||| ||||| ||| ||||||| || ||| |||||||||| |||||||||||||||||||  ||||| ||||||||||| 
tagtgtaattgctactggataaaaattgaaaacttaagatcactattatt--gtta--tatatgaatgcttcaaataatatcttgttaatctatgttatgacagTGTGAATGTCACTGTTGGTGAGAAAGAAGAACGGATGATGATCACCGGATTGCACACTGTCGTTGACATATTCTGTGTTGTATGTGGGTCCATTGTTGGG
















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|51052139|gb|CO819409.1|CO819409
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110702227|gb|EE080703.1|EE080703
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110390503|gb|EC955415.1|EC955415
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|77580160|gb|DV218980.1|DV218980
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110424401|gb|EC990761.1|EC990761
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110371533|gb|EC935633.1|EC935633
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110391310|gb|EC956275.1|EC956275
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
EST: gi|110388162|gb|EC952881.1|EC952881
EST:     GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGT                         TGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT
genomic: GCTTTTCACAGCAAACATGGGAAGGCTTATCTCTTTGATAAGGTgtaagtattc ... tgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgccagtcacatgcatcatttaattgatagtttgcttcgaaatgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGA
                        aattgat  putative branch site (score: 4)
                    atttaattgatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcactccttttatcaatgtctaagaaataaattcccttgcattttgccagtcacatgcatcatttaattgatagtttgcttcgaaatgcatgtcagTGTGAATGTCACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGA

- - -cactcct
- - - - - - - - -caatgtc
- - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - - - - - - - - -ttttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgc