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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGGACATCTGAAAGTTGCAGACTTTGGAGTTAGCAAGCTGCTGAAAGTTGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgcagttttggattacttgtcattgttttcaaaactttaatacatgaattattagcacaccctttctgtaaggagtcatgcatgttaaagtgg...

Basic information

species Vitis vinifera
transcript Vv10s0003g02060.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA15G09490.2 (Glycine max), 5'ss of exon 8
------------TCGGGACATCTGAAAGTTGCAGACTTTGGAGTTAGCAAGCTGCTGAAAGTTGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagta-tgcagtttt---ggattac--ttgtcattgttttcaaaactttaatacatgaattattagcacaccctttctgtaaggagtcat-gcatgttaaagtgg----------------------------------------------------------------------------------------
            || || || || ||||||||||||||||| ||||||||| |||||             |||||||||||||  | |||||||  || ||||| ||||| |||| ||  |||  || |   | | ||   || |      ||  || || | ||||  |||| |  |       | | |  ||  ||  | |  | || ||    |                                                                                          
TTGCGGGATGATTCTGGGCACCTAAAAGTTGCAGACTTTGGGGTTAGCAAGTTGCTGG------------CAGTTAAAGAAGACAAGCCTCTAACTTGCCAAGATACTTCCTgtgggtgctgcttttcttcagaactatcattatgcacacttgaaatacctaaatatctgaaatgctgtattttcttattcgttgggcataagagaatattgtcattattgtgacattttccatgtgctggacttttgcatgctgattcatggttttattttctgaaactgggaaattttttgtttttgtttatag

upper sequence: Vv10s0003g02060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G29520.1 (Glycine max), 5'ss of exon 8
------------TCGGGACATCTGAAAGTTGCAGACTTTGGAGTTAGCAAGCTGCTGAAAGTTGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagta-tgcagtttt---ggattac--ttgtcattgttttcaaaactttaatacatgaattattagcacaccctttctgtaaggagtcatgca-tgttaaagtgg-----------------------------------------------------------------------------------------
            || || || || ||||||||||||||||| ||||||||| |||||             |||||||||||||  | |||||||  || || || ||||| |||| ||  |||  || |   | | ||   || |  |   ||  || |  | ||||  |||| |  |       | | |      ||  | |   | | ||    |                                                                                           
TTGCGGGATGATTCTGGGCACCTAAAAGTTGCAGACTTTGGGGTTAGCAAGTTGCTGG------------CAGTTAAAGAAGACAAGCCTCTAACTTGCCACGATACTTCCTgtgggtgctgcttttcttcagaactatcattatgctcacttgaaatatctaaatatctgaaattctgtattttcttattcacggggcataagataatattgtcattattgtgacattttgcatgtgctggacttttacatgctgattcatggtttaattttctgaaactgggaattttttttgtttttgtttatag

upper sequence: Vv10s0003g02060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT4G18950.1 (Arabidopsis thaliana), 5'ss of exon 8
------------TCGGGACATCTGAAAGTTGCAGACTTTGGAGTTAGCAAGCTGCTGAAAGTTGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgcagttttggattacttgtcattg----ttttcaaaactttaatacatgaattattag--cacaccctttctgtaaggagtcatgc-atgttaaagtgg-----------------------
            || || |||||||||||||||||||||||||| ||||||||            |  ||| |||||||||||  | ||| | |  |||||||| | ||||||| ||||     |        ||| || | ||    |||| ||  ||||||| | |||  |  | |   | |   | |   | |   |   ||  ||  ||||                           
CTGCGGGATGATTCAGGGCATCTGAAAGTTGCAGACTTTGGAGTAAGCAAGCT------------TGTTACTGTTAAAGAAGACAAGCCTTTTACATGTCAAGACATTTCTTgtaagtactttttcgcacccaactagttactgtaaattttgaatgctttaattcttgatctgcttggttaaagagtcttcattactggatgtgttataataaaaatttatcggtgttatccacattatag

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|33407619|gb|CF213246.1|CF213246
EST:     TGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTT                         GTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG
genomic: TGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgc ... tcatgaacagGTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG
EST: gi|33407698|gb|CF213325.1|CF213325
EST:     TGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTT                         GTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG
genomic: TGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgc ... tcatgaacagGTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG
EST: gi|30255141|gb|CB971588.1|CB971588
EST:     TGTTAATACAGTTAAAGAAGATTACCCTCTAAGATCTCAAGAAACTTCTT                         GTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG
genomic: TGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgc ... tcatgaacagGTCGATATTTGGCTCCAGAGGTTTTTAAAAATGAAGCTTATGATACCAAGG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGGACATCTGAAAGTTGCAGACTTTGGAGTTAGCAAGCTGCTGAAAGTTGCTAATACAGTTAAAGAAGATTACCCTCTAATCTGTCAAGAAACTTCTTgtgagtatgcagttttggattacttgtcattgttttcaaaactttaatacatgaattattagcacaccctttctgtaaggagtcatgcatgttaaagtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctttc