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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcaccaattctggtttgtttatcttctaacataattgtgagaaaaaaaaaatgacaagggggtacctgatatccctgatgcctatcaacttgaa...

Basic information

species Vitis vinifera
transcript Vv06s0004g03140.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G07570.1 (Glycine max), 5'ss of exon 8
GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcaccaattctggtttgtttatcttctaacat-aattgtgagaaaaaaaaaatgacaagggggtacctgatatccctgatgcctatcaacttgaa
||||| ||||| ||||| || || || |||   |||||||| ||||| ||||| ||||| |||||||||||||||||||| |||| | || ||| |        |  |  || || || ||    ||     | ||  |||    ||   |  |    |       |  | |||||  
GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGGgtaattgctctaaatcttgacaacaagttatacaatattaagtggacaaacctctatatttcaacttagttaatttttaggcaataatgtgaccacttgc-

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA11G15900.1 (Glycine max), 5'ss of exon 8
GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcaccaattctggtttgtttatcttctaacat-aattgtgagaaaaaaaaaatgacaagggggtacctgatatccctgatgcctatcaacttgaa
||||| ||||| ||||| || || || |||   |||||||| ||||| ||||| ||||| |||||||||||||||||||| |||| | ||  || |        |  |  || || || ||    ||       ||  |||    ||   |  |    |       |  | |||||  
GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGGgtaattgctctaaaccttgacaacaagttatacaatattaagtggacaaacctctgtatttcaaattagttaattcttaggcaataatgtgaccacttgc-
















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|352772844|gb|FQ470459.1|FQ470459
EST:     GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG                         ATTCAGTACTGCTCAGAAATTAGACAAACTTGGGATGCGAGGAAGTGACAC
genomic: GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcac ... gacaatgcagATTCAGTACTGCTCAGAAATTAGACAAACTTGGGATGCGAGGAAGTGACAC
EST: gi|352764155|gb|FQ467725.1|FQ467725
EST:     GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG                         ATTCAGTACTGCTCAGAAATTAGACAAACTTGGGATGCGAGGAAGTGACAC
genomic: GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcac ... gacaatgcagATTCAGTACTGCTCAGAAATTAGACAAACTTGGGATGCGAGGAAGTGACAC
EST: gi|22010794|gb|BQ795828.1|BQ795828
EST:     GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG                         ATTCAGTACTGC
genomic: GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcac ... gacaatgcagATTCAGTACTGC
EST: gi|352781928|gb|FQ469225.1|FQ469225
EST:     GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG                         ATTCAGTACTGCTCAGAAATTAGACAAAC
genomic: GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcac ... gacaatgcagATTCAGTACTGCTCAGAAATTAGACAAAC
EST: gi|110729869|gb|EE106297.1|EE106297
EST:     GCTCATTCAAAAGGAATTACAGCATTTATCATCGAAAAGGGAATGCCTGG                         ATTCAGTACTGCT
genomic: GCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcac ... gacaatgcagATTCAGTACTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGGgtacttgcaccaattctggtttgtttatcttctaacataattgtgagaaaaaaaaaatgacaagggggtacctgatatccctgatgcctatcaacttgaa

- - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggggta