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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtgatgcctagcatcaattcaatttcttatttcaaggtgaaagccaattcttaagaattaagttgatatcctgttatctgatggtgggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG

Basic information

species Vitis vinifera
transcript Vv09s0002g01630.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 7
gtttgtgatgcctagcatcaattcaatt-tcttatttcaaggtgaaagccaattcttaagaattaagttgatatcctgttatctgatggtgggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG
 ||||   |   || |  |   | |||| ||  |||               ||||  | | | |||   || |     | || |  |  |  ||||||||||||||||||||||| || || ||||||||||| || ||||||||||  || |||||||||
-tttggtgtatataactgcctcttaattgtcacattgttttaaccttattgattcccatggaataacaggaaagggattaatattgtcatttgatttgcagGCAGCAAGTTTAAGGATTGCAGAGCAATATATTCAAGCTTTCAGTAACATAGCCAAGGAG
















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|18458599|gb|BM436877.1|BM436877
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|30324273|gb|CD007535.1|CD007535
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|110377134|gb|EC942193.1|EC942193
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|110393459|gb|EC958711.1|EC958711
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|30320908|gb|CD004170.1|CD004170
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|110385372|gb|EC949890.1|EC949890
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|30325554|gb|CD008816.1|CD008816
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
EST: gi|30327281|gb|CD010543.1|CD010543
EST:     GAGGAATTGAAATGGTGTCGCAGGCCCTTAAAGAAAGTGGGGGTGTAGAG                         GCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT
genomic: GAGGAATTGAAATGGTGTCGCGGGCCCTTAAAGAAAGTGGGGGTGTAGAGgtgagtttct ... ggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccaattcttaagaattaagttgatatcctgttatctgatggtgggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG
                                  atctgat  putative branch site (score: 4)
     attcttaagaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgatgcctagcatcaattcaatttcttatttcaaggtgaaagccaattcttaagaattaagttgatatcctgttatctgatggtgggatttgcagGCAGCAAGTTTAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - cctagca
- - - - - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - aagccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg