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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTCAGACACCCCATCACAGTCTGTTGAGCGGATGAGGGAAGCTCAAGCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttttgaacccttcatgcttcatttttttatatttatttatgattcatcaaagtggcatgaaagtggttcgagagaaggaaaaaagttttctgg...

Basic information

species Vitis vinifera
transcript Vv11s0078g00440.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0078g00440.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G24660.1 (Glycine max), 5'ss of exon 11
AGAATTCAGACACCCCATCACAGTCTGTTGAGCGGATGAGGGAAGCTCAAGCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttttg-aacccttcatgcttcatttttttatatttatttatgattcatcaaagtggca--tgaaagtggttcgagagaaggaaaaaagttttctgg
|||  ||||| || ||||||| |||||| ||| | |||||||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||||||||||||| ||||   ||  | | | | || | |||   | |  | ||||    |  |  ||||| |   || || ||  |  ||   ||   | |      |   
AGAGCTCAGATACACCATCACTGTCTGTGGAGAGAATGAGGGAAGCTCAAGCTCGTTTGCAGACACCCTATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgattttaacaattcctgaagttttaattta--aaaactgtttacatattgtagaagtgtctactggaattgtgtgtagttcagcgcacacacacacac-

upper sequence: Vv11s0078g00440.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA07G34600.1 (Glycine max), 5'ss of exon 11
AGAATTCAGACACCCCATCACAGTCTGTTGAGCGGATGAGGGAAGCTCAAGCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttttgaacccttcatgct--tcattttttta-tatttatttatgattcatcaaagtggcatgaaa-gtggttcgagagaaggaaaaaagttttctgg
|||  ||||| || ||||||| |||||||||| | |||||||||||||||||||| ||| ||||||| ||||||||||||||||| ||||||||||||||||||| ||||  |||  | ||  ||  | |||  |  | | || |||||  |    |  |  ||  || ||| | |   | ||        |  | ||   |  
AGAGCTCAGATACACCATCACTGTCTGTTGAGAGAATGAGGGAAGCTCAAGCTCGTTTGCAGACACCATATCTTGTTCTTAGTGGTCATGTTAAACCAGGgtatgatttt--aactttacagactaataattcctgaagttttaatttaaaaactgtttacatgtaataaaatgagaaactaggagcatgcatcatttcatt--

upper sequence: Vv11s0078g00440.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G16780.1 (Arabidopsis thaliana), 5'ss of exon 11
AGAATTCAGACACCCCATCACAGTCTGTTGAGCGGATGAGGGAAGCTCAAGCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttttgaacccttcatgcttcatttttttatatttatttatgattcatcaaagtggcatgaaagtggttcgagagaaggaaaaaagttttctgg-----
| || |||||||| ||||| ||||||||| |  | ||||| |||||||||||||  ||||| || || || ||||| || ||||| ||||| |||||||||||| | |     |  ||||||  |||| ||||   | ||    |       ||  ||||| |    |  |  ||  |   |   | |   |||   |       
AAAACTCAGACACACCATCGCAGTCTGTTCAAAGAATGAGAGAAGCTCAAGCTCAATTGAAAACTCCTTACCTTGTCCTCAGTGGCCATGTCAAACCAGGgtatacat-----atgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaactaacacatatttgttacattattcag

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|33401769|gb|CF207396.1|CF207396
EST:     GCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGG                         CCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
genomic: GCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttt ... ttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
EST: gi|33401847|gb|CF207474.1|CF207474
EST:     TAGTGGGCATGTTAAACCAGG                         CCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
genomic: TAGTGGGCATGTTAAACCAGGgtatgctttt ... ttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
EST: gi|34362752|gb|CF404337.1|CF404337
EST:     AGTGGGCATGTTAAACCAGG                         CCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
genomic: AGTGGGCATGTTAAACCAGGgtatgctttt ... ttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
EST: gi|110415341|gb|EC981241.1|EC981241
EST:     GGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGG                         CCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
genomic: GGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttt ... ttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
EST: gi|110366700|gb|EC930616.1|EC930616
EST:     GCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGG                         CCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC
genomic: GCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttt ... ttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCC

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATTCAGACACCCCATCACAGTCTGTTGAGCGGATGAGGGAAGCTCAAGCTCGGTTGAAGACACCCTATCTTGTTCTTAGTGGGCATGTTAAACCAGGgtatgctttttgaacccttcatgcttcatttttttatatttatttatgattcatcaaagtggcatgaaagtggttcgagagaaggaaaaaagttttctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaa