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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCGGCGAGGTGCCGGAAGAGCCGGTTGTTTCCAAGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttcattttctgctcttccttcttgggttttgcactgtttggttactcagatagaattttaaaccctagggtttgccctgtttgcgacctcacat...

Basic information

species Vitis vinifera
transcript Vv05s0049g01840.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G037698_T01 (Zea mays), 5'ss of exon 2
TGTCCGGCGAGGTGCCGGAAGAGCCGGTTGTTTCCAAGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttcattttctgctcttccttcttgggttttgcactgtttggttac-tcagatagaattttaaaccctagggtttgccctgtttgcgacctcacat-----------------------------------------------
| ||||| ||||||||||| |||||||| || || ||||| || |||||||||||||||   ||  | |||||| |  ||||   |||      | |    ||  ||    ||| | | |      | |||  |    |  |  | ||| ||    |  |     || | || | ||||   |  ||                                               
TCTCCGGTGAGGTGCCGGACGAGCCGGTGGTGTCGAAGAAGTCGGGGCTTCTCTTCGAGCGGCGGCTCATCGAGCGCTACATTGAGgt-----ccgtagcttggcctcagatctcgcgctgcaatttttttattgggattgggaaaaatgtttgtgctaaattcatgtcatggtggcgatgcccaatgtttatgctaaattcatgtcgtgatggcgatgcccacaacattgcag

upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 2
TGTCCGGCGAGGTGCCGGAAGAGCCGGTTGTTTCCAAGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttcattttctgctcttccttcttgggttttgcactgtttggttactcagatagaattttaaaccctagggtttgccctgtttgcgacctcacat--------
| ||||||||||||||||| |||||||| || || ||||| || ||||| |||||||||   ||  | |||||| |  ||||   |||      | |  | || |||    ||||||| |  |   | |||  ||    | ||    ||||    |  |     || | ||    |||   ||||         
TCTCCGGCGAGGTGCCGGACGAGCCGGTCGTGTCGAAGAAGTCGGGGCTACTCTTCGAGCGGCGGCTCATCGAGCGCTACATTGAGgt-----ccgtagtttggtctcagatcttgggctgggattttttttatttggaaaatgttttttttttgctaaattcatgtcgtgacgccgatgccacaacattgcag
















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|110729437|gb|EE105388.1|EE105388
EST:     AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACGTATCG                         GATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
genomic: AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttca ... ctttgtatagGATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
EST: gi|71858292|gb|DT007347.1|DT007347
EST:     AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACGTATCG                         GATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
genomic: AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttca ... ctttgtatagGATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
EST: gi|161710544|gb|FC058133.1|FC058133
EST:     AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACGTATCG                         GATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
genomic: AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttca ... ctttgtatagGATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
EST: gi|110687481|gb|EE064937.1|EE064937
EST:     AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACGTATCG                         GATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT
genomic: AGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttca ... ctttgtatagGATTATGGAAAATGTCCAATTACAGGGGAGCCACTAACTATGGACGATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCCGGCGAGGTGCCGGAAGAGCCGGTTGTTTCCAAGAAATCTGGGCTTCTCTTCGAGAAACGTTTGATCGAGAGACACATATCGgtattcttcattttctgctcttccttcttgggttttgcactgtttggttactcagatagaattttaaaccctagggtttgccctgtttgcgacctcacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatagaa