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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaatgaaactaagcttcccaatacgcctgcttaatcaatgattttatagatacattttgataatacttgtttttgtcttacttgatgagcaatgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTCTGCCGAAACTTATTGCCTGGTTCACTTCCCAAGCTTGATCAG

Basic information

species Vitis vinifera
transcript Vv13s0074g00190.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00190.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G13240.1 (Glycine max), 3'ss of exon 6
gtataaatgaaactaagcttcccaatacgc-ctgcttaatcaatgattttatagatacattttgataatacttgtttttgtcttacttgatgagcaatgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTCTGCCGAAACTTATTGCCTGGTTCACTTCCCAAGCTTGATCAG
||| | ||     ||| |   | | | ||   |||||| ||  |  |||  |   |  | ||  |   | |||||| ||   ||   |  ||  |||  ||| |||||||||| || |||||||||||||||||||| |||||| | ||||||   ||||| ||||| |||||| ||||||| || ||||| || |||||
gtacatatccctataatcgatcaactgcgtgttgcttattcttttctttggttattttagttaaaatcttcttgttattaatttgaatc-tgttcaacattt-ccagGTTTCCTTTATTTGGAAAGAAATACCAGCTAAAATTTGCTAATGATGTCTCTGCTGAAACCTATTGCTTGGTTCATTTTCCAAGTTTCATCAG

upper sequence: Vv13s0074g00190.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G41590.1 (Glycine max), 3'ss of exon 6
gtataaatgaaactaagcttcccaatacgc-ctgcttaatcaatgattttatagatacattttgataatacttgtttttgtcttacttga---tgagcaatgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTCTGCCGAAACTTATTGCCTGGTTCACTTCCCAAGCTTGATCAG
||| | ||     |||     | | | |    |||||| ||  |  |||  |   |  | ||  | ||| ||| || |  | | | ||||   ||  |||  ||| |||||||||| || |||||||||||||||||||| |||||| | ||||||   ||||| |||||  ||||| ||||||| || ||||| || |||||
gtacatatccctataattggtcaactgcatgttgcttattctgttctttggttattttagtt--aaaat-cttcttgtcatttaatttgaatctgttcaacattt-ccagGTTTCCGTTATTTGGAAAGAAATACCAGCTAAAATTTGCTAATGATGTCTCTGCTGAAACCCATTGCTTGGTTCATTTTCCAAGTTTCATCAG
















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|110685378|gb|EE062046.1|EE062046
EST:     TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAA                         GTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC
genomic: TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAAgtataaatga ... tgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC
EST: gi|30126088|gb|CB911427.1|CB911427
EST:     TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAA                         GTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC
genomic: TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAAgtataaatga ... tgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC
EST: gi|110722057|gb|EE097952.1|EE097952
EST:     TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAA                         GTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTGCCAATGATACTTC
genomic: TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAAgtataaatga ... tgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC
EST: gi|110703995|gb|EE081418.1|EE081418
EST:     TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAA                         GTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTGCCAATGATACTTC
genomic: TGCATTCGATCAGAGAGCTATATGATCACTTTTGAAGTTGAAGAAGAGAAgtataaatga ... tgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatacattttgataatacttgtttttgtcttacttgatgagcaatgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTCTGCCGAAACTTATTGCCTGGTTCACTTCCCAAGCTTGATCAG
                                             tgttttcc  CT-rich tract
      attttgataatacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaatgaaactaagcttcccaatacgcctgcttaatcaatgattttatagatacattttgataatacttgtttttgtcttacttgatgagcaatgttttccagGTTTCCATTTTTTGGAAAGAAATACCAGCTGAAATTTTCCAATGATACTTCTGCCGAAACTTATTGCCTGGTTCACTTCCCAAGCTTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT