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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatttcttcacttccaattgtcacaatcagttggaagcctttttcactaattattgcataaaacttctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGTTGCTTCTGAAGCAGTAGCTGATAGAAGATCTTCTTTCCAAATTAAACGA

Basic information

species Vitis vinifera
transcript Vv16s0039g02260.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02260.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA11G01410.1 (Glycine max), 3'ss of exon 4
gtattttatttcttcacttccaattgtcacaatcagttggaagcctttttcactaattattgc--ataaaacttctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGTTGCTTCTGAAGCAGTAGCTGATAGAAGATCTTCTTTCCAAATTAAACGA---
|||  | |    |||| ||| ||| |     ||   |   ||||  ||   ||| ||| |  |  ||     || | ||||||| ||||| || |||| ||||||| |||| || ||||| |||||||| ||||  |||||||||||||||||||| ||||||||||   |||| ||||| |||   
gtacataacactttcatttctaatggatgttat-gttataaagctattcatactgattgtcacccatgttcattatcttttcagTGTAGAGAATGATGAAAGAGAATTGCTAGTTGCTGTGAGCTTTGGGCTAGCAGCTTCTGAAGCAGTAGCTGACAGAAGATCTT---TCCAGATTAAGCGATGG

upper sequence: Vv16s0039g02260.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA01G43940.1 (Glycine max), 3'ss of exon 4
gtattttatttcttcacttccaattgtcacaatcagttggaagcctttttcactaattattgc--ataaaacttctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGTTGCTTCTGAAGCAGTAGCTGATAGAAGATCTTCTTTCCAAATTAAACGA---
|||  | |    |||| ||| ||| |  |  ||   |   ||||  |    ||| ||| |  |  ||     || | ||||||| ||||| || |||| ||||||| |||| || ||||| |||||||| ||||  |||||||||||||||||||| ||||||||||   |||| ||||| |||   
gtacataacactttcatttctaatggatattat-gttataaagctatccatactgattgtcacccatgttcattatcttttcagTGTAGAAAATGATGAAAGAGAATTGCTAGTTGCTGTGAGCTTTGGGCTAGCAGCTTCTGAAGCAGTAGCTGACAGAAGATCTT---TCCAGATTAAGCGATGG
















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|71866418|gb|DT015473.1|DT015473
EST:     CCAGTGCTTAGAGTGGAAGGGAGTCACTTGCTTGCTGCTGTTGTTGTCAG                         AGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGC
genomic: CCAGTGCTTAGAGTGGAAGGCAGTCACTTGCTTGCTGCTGTTGTTGTCAGgtattttatt ... ctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaatcagttggaagcctttttcactaattattgcataaaacttctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGTTGCTTCTGAAGCAGTAGCTGATAGAAGATCTTCTTTCCAAATTAAACGA
                       cactaat  putative branch site (score: 2)
                                          cttctattttc  putative PPT
                  tttttcactaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttatttcttcacttccaattgtcacaatcagttggaagcctttttcactaattattgcataaaacttctattttcagAGTAGATAAGGATGGAAGAGAACTGCTTGTCGCTGTAAGCTTTGGACTAGTTGCTTCTGAAGCAGTAGCTGATAGAAGATCTTCTTTCCAAATTAAACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT