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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattataagcttaatttgtgtttggattcttcttccgagtctttcatctggactttggtcataatgaacctaaaagcttttggagggtttgttataatgaacatttctgatcatgcacaaatccaattaatacttgtttctgttatatttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTTATGACAAATGCTTACAAGTATTTGATTGAGGCAGGAGGTTTGGAGGAGG

Basic information

species Vitis vinifera
transcript Vv13s0019g05120.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G54940.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaattataagcttaatttgtgtttggattcttcttccgagtctttcatctggactttggtcataatgaacctaaaagcttttggagggtttgttat--aatgaacatttctgatcatgcacaaatccaattaatacttgtttctgttatatttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTTATGACAAATGCTTACAAGTATTTGATTGAGGCAGGAGGTTTGGAGGAGG
                                                                             | ||||     |||  | |   |||    | |  |||       |   |    | || | || |||    ||||| |   |  ||||||||  || ||||||||  ||||| |||| ||| || |  || || || ||||||||||| ||| |||||||||| ||||||||||| || || || |
-------------------------------------------------------------------------gtctgtttttaatccgttaatcaacgaatttgtactcttgacttgatccttgtaatttgaaaatttatttggtatatatatgagtatagTGCGATCCAAAGGACAAGAAAGCATGCGACAATGGATGTGGCGGGGGACTGATGACAAATGCCTACGAGTATTTGATGGAGGCAGGAGGATTAGAAGAAG
















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|110393160|gb|EC958177.1|EC958177
EST:     AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATG                         TGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
genomic: AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATGgtaattataa ... ttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
EST: gi|110401460|gb|EC968070.1|EC968070
EST:     AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATG                         TGCGATATAAGGGACAAGGCCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
genomic: AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATGgtaattataa ... ttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
EST: gi|110364611|gb|EC927994.1|EC927994
EST:     AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATG                         TGCGATTTAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
genomic: AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATGgtaattataa ... ttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
EST: gi|110397716|gb|EC963559.1|EC963559
EST:     AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATG                         TGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT
genomic: AGAAACTTCTCACTCTAAGTGAGCAACAACTTGTAGACTGTGATCACATGgtaattataa ... ttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgatcatgcacaaatccaattaatacttgtttctgttatatttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTTATGACAAATGCTTACAAGTATTTGATTGAGGCAGGAGGTTTGGAGGAGG
                     aattaat  putative branch site (score: 3)
                                          tatttttctc  putative PPT
                     aattaatacttgtttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattataagcttaatttgtgtttggattcttcttccgagtctttcatctggactttggtcataatgaacctaaaagcttttggagggtttgttataatgaacatttctgatcatgcacaaatccaattaatacttgtttctgttatatttttctcaagTGCGATATAAGGGACAAGACCGCATGTGACAGTGGTTGCGAGGGAGGCCTTATGACAAATGCTTACAAGTATTTGATTGAGGCAGGAGGTTTGGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG