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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcacatcaggctagctctccttttacaatgttgtatgtgatgattgtttttttttatttttattttatgtaattgctgcttggactactctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG

Basic information

species Vitis vinifera
transcript Vv08s0056g01150.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 7
attcacatcaggctagctctccttttacaat--gttgtatgtgatgattgtttttttttatttttattttatgta-attgctgcttggactact--ctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG-------------
  | | |||    |||  |    | || | |  |   || |  |||  || |  ||  ||     ||||   | | ||| |    | || |  |  ||    |||||||||||||  |||||||||||||| |||||||| ||  |||| ||||| || || ||||  || ||||||||    |||||| |              
--taaaatcg---tagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 7
attcacatcaggctagctctccttttacaat--gttgtatgtgatgattgtttttttttatttttattttatgta-attgctgcttggactact--ctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG
  | | |||    |||  |    | || | |  |   || |  |||  || |  ||  ||     ||||   | | ||| |    | || |  |  ||    |||||||||||||  |||||||||||||| |||||||| ||  |||| ||||| || || ||||  || ||||||||    |||||| | 
--taaaatcg---tagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G157263_T01 (Zea mays), 3'ss of exon 7
attcacatcaggctagctctccttttacaatgttg-tatgtgatgattgtttttttttatttttattttatgtaattgctgcttggactactctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG
       |     |   | ||| | ||    |||| ||    |  ||  ||   |  | | | | | |||   ||    ||| | |  | ||    | |||||||||||||  ||| |||||||||||||||| || || |||||||||||| || | |||||||| || |||||  | |||||| ||
------gtttacttgtatttccctataattagttggtaccctactatgcttcgctcgtctgtgtgtcttactaaaca--tgcatcgtttcctg---cgcagCCTCCTGAAGTCTGGGACGGTGGCGTCGGGTTCGTGTCGAAGGAAATGATCCAGACTCATTGCCCAGCGCCTGCCGCCGACATTCAG

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
------------attcacatcaggcta-gctctccttttacaatgttgtatgtgatgattgtttttttttatttttattttatgtaattgctgcttg--gactactctcccac-agCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG
            |||||  |     |  | |   |   |  ||     ||    | ||    ||| |  ||  |||  ||  |||  ||  ||  |   | |||       |  ||||||| |||| |||| | ||||| || || |||||||| |||||||||||  || | ||||||||||||||||||||||| ||| ||
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG

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|110691213|gb|EE069059.1|EE069059
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|37188279|gb|CF607628.1|CF607628
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAG                         CCTCCTGAAGCATGGAATGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|33406972|gb|CF212599.1|CF212599
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGT-GATGTTTGTATCGATCGAAATGAT
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGG-GTTTGTATCCAAGGAAATGAT
EST: gi|33407295|gb|CF212922.1|CF212922
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|110375510|gb|EC940502.1|EC940502
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|110384799|gb|EC949262.1|EC949262
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|110397391|gb|EC963126.1|EC963126
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|33406880|gb|CF212507.1|CF212507
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTTTGAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|351015566|gb|FQ426808.1|FQ426808
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAG                         CCTCCTGAAGCATGGAATGGTGG
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGG
EST: gi|33407387|gb|CF213014.1|CF213014
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
EST: gi|110371220|gb|EC935065.1|EC935065
EST:     TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTTAATCAG                         CCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC
genomic: TTTCTGCCAGCTACCCTGATCACTTTAAAGTTTACTATGTTCTGAATCAGgtcccttacc ... tctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttttttttatttttattttatgtaattgctgcttggactactctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG
                                         ctactctccc  CT-rich tract
     tttttttatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcacatcaggctagctctccttttacaatgttgtatgtgatgattgtttttttttatttttattttatgtaattgctgcttggactactctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- -cacatca
- - - - - - - - ctctcct
- - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgg