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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataacttactctctctgccttcacatttccaactttttaaaaaaaaaatctttttttctttattcaagttataactagttttatatctccattccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTGCTTTTGATGCTGCTGCCAACGGACCTACTGACTCATATAGCAACTCGTC

Basic information

species Vitis vinifera
transcript Vv12s0035g01740.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 21
ataacttactctctctgccttcacattt-ccaactttttaaaaaaaaaatctt----tttttctttattcaagttataactagtttt-atatctccattccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTGCTTTTGATGCTGCTGCCAACGGACCTACTGACTCATATAGCAACTCGTC-
      ||  | || |  | |   || |  ||  |   | |  ||| |||  |    | ||  ||| || |  || ||  || |||  | |     |||  | |||| |||||||| |||| | | |||||||||||||||||||| ||||| ||||| |||||| |||||||||| || || |   ||    |   | |    |  
------tatccacttttgcgtagaatctgtcatatgcatcagtaaagaattataggctattattttgttaactttttatataatttcgacaaacaaatttatgcagAAAGCAGCCCAAGAAGCTCTGGACCCTCATCAGGTGATGATTGGAGGTCTGCATTTGATTCTGCTGCCAATGGTCCAAGCAACCTG-ACGTCTAGGTATGG

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 21
---ataacttactctctctgccttcacatttccaactttttaaaaaaaaaatctttttttctttattcaagttataactagttttatatctccattccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTGCTTTTGATGCTGCTGCCAACGGACCTACTGACTCATATAGCAACTCGTC-
   |  ||||   |       ||||| ||     | |   |||  | ||  | || |||| || | |     ||||| |   |  | |     |||  | |||| ||||||||  ||| | | ||||||||||||| |||||| ||||| ||||| |||||| |||||||||| || || |  ||||       | |    |  
gtaaccacttttgcatagaatcttcatatgcatcagtaaataattataagctattattttgttaactttttatataatt---tcgacaaacaaatttatgcagAAAGCAGCCCAGGAAGCTCTGGACCCTCATCAGTTGATGATTGGAGGTCTGCATTTGATTCTGCTGCCAATGGTCCAAGCGACTTGC-CGTCTAGGTATGG
















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|160482004|gb|EY254989.1|EY254989
EST:     TGACAACCGTGCAGCAGCTGCTTCTAGCAGCTGGTCCAATGGTGGTGCAG                         AGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG
genomic: TGACAACCGTGCAGCTGCTGCTTCTAGCAGCTGGTCCAATGGTGGTGCAGgtattatagc ... attccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG
EST: gi|110412438|gb|EC978188.1|EC978188
EST:     GCTTCTAGCAGCTGGTCCAATGGTGGTGCAG                         AGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG
genomic: GCTTCTAGCAGCTGGTCCAATGGTGGTGCAGgtattatagc ... attccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG
EST: gi|30135425|gb|CB920763.1|CB920763
EST:     TGACAACCGTGCAGCTGCTGCTTCTAGCAGCTGGTCCAATGGTGGTGCAG                         AGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG
genomic: TGACAACCGTGCAGCTGCTGCTTCTAGCAGCTGGTCCAATGGTGGTGCAGgtattatagc ... attccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctttttttctttattcaagttataactagttttatatctccattccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTGCTTTTGATGCTGCTGCCAACGGACCTACTGACTCATATAGCAACTCGTC
                       ttataac  putative branch site (score: 2)
                                      tatctccattccttc  putative PPT
     tttttttctttattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataacttactctctctgccttcacatttccaactttttaaaaaaaaaatctttttttctttattcaagttataactagttttatatctccattccttcagAGAGCAGCCCGAGAACCCCCGGACCCTCATCAGGTGATGACTGGAGATCTGCTTTTGATGCTGCTGCCAACGGACCTACTGACTCATATAGCAACTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - ctctctc
- - - - - - - - -ccttcac
- - - - - - - - - - - - - -tccaact
- - - - - - - - - - - - - - - - - - - aaaaaaa