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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggaattgagcatggtcgttgcgaaaattttgcggctggttttggttttgttgacagtttcttttgttgttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGA

Basic information

species Vitis vinifera
transcript Vv11s0016g00900.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------gtttgtggaattg------agcatggtcgttgcgaaaattttgcggctggttttggttttgttgacagtttcttttgttgttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGA
                                                                              | || || |||      || |  |    |  |     || |  |||  ||     |   |    |  |  || |  |||| ||| |||||||||| |||||| |||||||||||||||| |||||||| |||||  | || || || ||||    | | ||| | || ||||| || |||||||| |
gtgagttttttgtttttaaaaaaagaacatttttttaatactttatttgggggggttattttttgtgttttagttacatggtagagttggtagatagtactgcatctatgtgttattggaagctaattgaaactaattgaggatgtgattgtaatgttattgcagATTCCGGCACCGAAGAGAGGTGAGATTGTGAGACAGATTGGTGAAGCATTGAGGGCCAAGTTGGATCCTTTGGGTAGACTGGTGTCTCTTGAGATGGGAA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 1
-------------gtttgtggaat-tgagcatggt--cgttgcgaaaattttgcggctggttttggttttgttgacagttt-cttttgttgttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGA
                      || |   | ||||  | | |     | | | ||     ||      |  ||||   | | ||| |  |||||||| |||| ||||| |||||| |||||||||||||||| |||||||| |||||  | || || |||||||    | | ||| |||| ||||| || |||||||| |
gatcaaacattcaacccaccttatatctccctggtaacctagtactgaatctacgtgctattggaaactaattgaggatgtgcttgtaatgttgttgcagATACCGGCACCGAAGAGAGGTGAGATTGTGAGACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAA
















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|30128999|gb|CB914338.1|CB914338
EST:     ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAG                         ATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
genomic: ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAGgtttgtggaa ... gttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
EST: gi|30129010|gb|CB914349.1|CB914349
EST:     ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAG                         ATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
genomic: ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAGgtttgtggaa ... gttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
EST: gi|110701993|gb|EE080197.1|EE080197
EST:     ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAG                         ATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
genomic: ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAGgtttgtggaa ... gttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
EST: gi|110725486|gb|EE102039.1|EE102039
EST:     ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAG                         ATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT
genomic: ACGAGGAGGGGCTGATGGCTTGCAGTGAAGCAGCAAAGACGTGGATGAAGgtttgtggaa ... gttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattttgcggctggttttggttttgttgacagtttcttttgttgttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGA
                         tgttgac  putative branch site (score: 3)
                                  tttcttttgttgtt  putative PPT
                                  tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggaattgagcatggtcgttgcgaaaattttgcggctggttttggttttgttgacagtttcttttgttgttgttgaagATTCCGGCGCCGAAGCGAGGTGAGATTGTGAGGCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG