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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccacggttcagagcacatcaaagaattttgttttgattcattggtttatctaatacgtgtcttttacatctaaggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 2
gccacggttcagagcacatcaaagaattttgttttgattcattg-gtttatctaatacgtgtcttt----tacatctaaggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA
      |  | | |  || ||   ||||      | |||||||  | |   ||| | | ||| ||     |   | ||  |   ||  | |  |   |  | ||||| ||| | ||||| ||||||||||  ||| | ||  |||| || |||||||| || ||||||||||| ||||| ||||||||||||
-----tgaactgggggcaccagtcaattcctcactaattcatttcgatgcactactgcctgttttactaatctgtttattgtctttcctgttgaatggaacgcagGATGAGAAGACAAAGTCCTGGAAGAGCTTAGTGAATGTTGCTGTGTCGGGTGCAGCAGGGATGATATCAAATCATCTGCTTTTCAAA

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G34150.2 (Glycine max), 3'ss of exon 2
gccacggttcagagcacatcaaagaattt----tgttttgattca-ttggtttatctaatacgtgtcttttacatctaaggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA
      || ||    |  | |  |  | |    |||| | |  || ||   ||    | |   ||   ||| | ||   | ||  ||    |||||| ||  |||||||| || |||| ||||||||||||||||||||||||||||||||| ||||||||||| |||||  | ||||| || |||||||| 
-----tgtgcatgtgaatttagtggctcttagatgttatcagacagttaaatttgtcagtctatgctatttgcctcattgaaatatttggccaatgtttttgcagGAAGAAGAGACAAGATCCTGGAAGAAATTAATTAACATTGCAGTCTCAGGTGCTGCTGGAATGATTGCAAATCATCTACTTTTCAAG

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 2
gccacggttcagagcacatcaaaga-attttgttttgattcattggtttatctaatacgtgtcttttacatctaa--ggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA
  | |  | ||     | |     | ||    | |   |||| |     |    ||||    | |  |||  |||  | ||   |    |||||| ||  |||||||| || |||| ||||||||||||||||||||||||||||||||| ||||||||||| |||||  | || || || |||||||| 
-tctctttccaattttccttttttatatacaatataatttcaataaaaaaa--gatacacaacatgaacagttaattgaaatacttggccaatgtttttgcagGAAGAAGAGACAAGATCCTGGAAGAAATTAATTAACATTGCAGTCTCAGGTGCTGCTGGAATGATTGCAAACCATCTACTTTTCAAG

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|110728729|gb|EE104550.1|EE104550
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
EST: gi|351028003|gb|FQ425904.1|FQ425904
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
EST: gi|32249928|gb|CD715747.1|CD715747
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
EST: gi|110382693|gb|EC947010.1|EC947010
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
EST: gi|110389983|gb|EC954863.1|EC954863
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
EST: gi|27578522|gb|CB001217.1|CB001217
EST:     TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCG                         GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT
genomic: TCAAGCCCGAGTGCTTTGGGGTCTTCTGCACCACATATGATCTCAAGGCGgtaagtttga ... gtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctaatacgtgtcttttacatctaaggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA
   atctaat  putative branch site (score: 3)
                               aagtttatatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccacggttcagagcacatcaaagaattttgttttgattcattggtttatctaatacgtgtcttttacatctaaggaagtttatatcaatgtgttcacagGAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - -caaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaggaa