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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctggattttccatagcacattcaatgaaattatctgattctagctatgcatttataatgtgttaaacaaaattatctgattctgttttattgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G03080.3 (Glycine max), 3'ss of exon 10
ttctggattttccatagcacattcaatgaaatt--atctgattctag--ctatgcatttataatgtgttaaacaaaattatctgattctgtt-ttattgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG-----
    |||||      |  |  ||  |     ||  |||| ||| | |    |    || ||||   | |||| | | ||     ||| |  | || || |  |||| |||||| | |  ||||| || ||||||||| | ||| |||||||||| || ||||||||  |||| || ||||||||  | ||||||||||||     
----ggattaattggaataagttagacttttttccatcttattttggggtaaaatgttaataaaa-gataaatatactttgacaattttcctgtttttttattagGCTTGGGACTTGGGGATATATTGAAGCCTGATCTAATAATGCCATTGATGGATACATTACCTTTGGAGCAGCGTTTAGCTCCCTACTTACCTGAGGTACA

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G03080.1 (Glycine max), 3'ss of exon 10
ttctggattttccatagcacattcaatgaaatt--atctgattctag--ctatgcatttataatgtgttaaacaaaattatctgattctgtt-ttattgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG
    |||||      |  |  ||  |     ||  |||| ||| | |    |    || ||||   | |||| | | ||     ||| |  | || || |  |||| |||||| | |  ||||| || ||||||||| | ||| |||||||||| || ||||||||  |||| || ||||||||  | ||||||||||||
----ggattaattggaataagttagacttttttccatcttattttggggtaaaatgttaataaaa-gataaatatactttgacaattttcctgtttttttattagGCTTGGGACTTGGGGATATATTGAAGCCTGATCTAATAATGCCATTGATGGATACATTACCTTTGGAGCAGCGTTTAGCTCCCTACTTACCTGAG
















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|87584845|gb|DY473849.1|DY473849
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTAATTTGATAC
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATAC
EST: gi|110395278|gb|EC960936.1|EC960936
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|18459586|gb|BM437864.1|BM437864
EST:     TGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
genomic: TGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|33405732|gb|CF211359.1|CF211359
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTAATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|110391622|gb|EC956610.1|EC956610
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTAATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|351028718|gb|FQ433148.1|FQ433148
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG
EST: gi|161716363|gb|FC068095.1|FC068095
EST:     GATGGTGCTGGAGATCCAGATGAAG                         GTTTGGGATTAGCAGATATTTTAAAGCCTAATTTGATACTGCCATTGATTG
genomic: GATGGTGCTGGAGATCCAGATGAAGgtaatgattt ... attgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgcatttataatgtgttaaacaaaattatctgattctgttttattgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG
                              atctgat  putative branch site (score: 4)
                                         ttttatt  putative PPT
      atttataatgtgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctggattttccatagcacattcaatgaaattatctgattctagctatgcatttataatgtgttaaacaaaattatctgattctgttttattgttctagGTTTGGGATTAGCAGATATTTTAAAGCCTGATTTGATACTGCCATTGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG

- - - - - - - - -cacattc
- - - - - - - - - - - - aatgaaa
- - - - - - - - - - - - - - - - - -ctgattc
- - - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa