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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaaagggaaaacccagattctttaaacaataccttaaaattcactccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT

Basic information

species Vitis vinifera
transcript Vv12s0028g01550.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G13360.1 (Glycine max), 3'ss of exon 3
gtatttt--tttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaaagggaaaacccagattctttaaacaataccttaaaattcactcccttt--cagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT
||| | |  ||| |  |||| || | || ||| |||     ||  ||  |    |     |    |  |    | |  || | |         |||    |||   || | |  ||||| ||| ||||||| || ||| | ||||||| |||  ||||| |||||||||||||||| ||| |||||||| | ||| ||||  |||||||| | || |
gtactatgctttatagttatatttaatttaatctataggagctagcaggagttaaggatagtggtgatactttctatgttatctttgtttcttcttcgtcttcttcccttatggcagGTTTTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTAAGGAAGCTCTCTCAGCTTCCAGAAAAAT

upper sequence: Vv12s0028g01550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G44390.2 (Glycine max), 3'ss of exon 2
gtatttttttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaa-agggaaaacccagattctttaaacaataccttaaaattcactcccttt-cagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT-------------------------
   |  | | |||| || ||  |||| |||||| |||       | |    ||| |  ||   | ||| |     ||| | ||  |   || |||    |   | |   |  |||||  || ||||||| || ||| | ||||||| |||  ||||| |||||||||||||||| ||| ||||||||   ||| |||| ||||||||| | || |                         
--gtaatatgctttataattgtattt-aatttaattt-------ataggagcaagcaggaggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcaggttgtactaaaccagattgtgttagGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAATACAGAAGAGATGCTCTTCCAACGCT

upper sequence: Vv12s0028g01550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G44390.1 (Glycine max), 3'ss of exon 2
gtatttttttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaa-agggaaaacccagattctttaaacaataccttaaaat-tcactccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT
   |  | | |||| || ||  |||| |||||| |||       | |    ||| |  ||   | ||| |     ||| | ||  |   || |||    | |  |   ||  |||||  || ||||||| || ||| | ||||||| |||  ||||| |||||||||||||||| ||| ||||||||   ||| |||| ||||||||| | || |
--gtaatatgctttataattgtattt-aatttaattt-------ataggagcaagcaggaggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAAT

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|161711520|gb|FC059498.1|FC059498
EST:     ATCTTGATCATGCTTTGCCAAAGCAAACTGTGGAGATCCTGTTGCTGAAG                         GTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTA
genomic: ATCTTGATCATGCTTTGCCAAAGCAAACTGTGGAGAACCTGTTGCTGAAGgtattttttt ... tccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTA
EST: gi|110373369|gb|EC937597.1|EC937597
EST:     ATCTTGATCATGCTTTGCCAAAGCAAACTGTGGAGAACCTGTTGCTGAAG                         GTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTT
genomic: ATCTTGATCATGCTTTGCCAAAGCAAACTGTGGAGAACCTGTTGCTGAAGgtattttttt ... tccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaagggaaaacccagattctttaaacaataccttaaaattcactccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT
                                        ttcactccctttc  CT-rich tract
                     tttaaacaatacctta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaaagggaaaacccagattctttaaacaataccttaaaattcactccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT