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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgatcaaagctatttgcatatatgtttcatttttcacatgccgggcaccaggcctttgctttattatttccagaccctaaaccttcctttgattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCCGAGCTCAGGCATCGGGCACTACTTGCTAGAAACAAGCAGGATTAGTTTT

Basic information

species Vitis vinifera
transcript Vv12s0035g00810.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00810.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G34350.2 (Arabidopsis thaliana), 3'ss of exon 3
gttagtgatcaaagc-tatttgcatatatgtttcatttttcacatgccgggcaccaggcctttgctttatta-tttccagaccctaa--accttcctttgattttg-cagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCCGAGCTCAGGCATCGGGCACTACTTGCTAGAAACAAGCAGGATTAGTTTT
         |||| | || |  ||||  || | ||| | |    |           |  || ||  |  | | | |  | |  || |      |  | || ||||| ||| | || || ||||| ||  | |||    || |  | |||||||||||||| |||||||||||||| |||   ||||||   | |||| |||| |  |   
---------caaaccatagtaccatac-tgatccatgtcttgtttaggattttaacgaactatgtgtagtgaatgtggaaaatctgatggaggtgttgtgtttttgacagATAAACACACTCTTTTCGCTTTGCTACTTAATCGTAAAGTGGAAAAGAGCTGAGCTCAGGCATCGCGCAAGGCTTGCTCATACCAAGGAGGAATGATCCC
















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|110377298|gb|EC942362.1|EC942362
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|110403121|gb|EC964315.1|EC964315
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|26265230|gb|CA816293.1|CA816293
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|110688760|gb|EE067680.1|EE067680
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCT
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|161710777|gb|FC059860.1|FC059860
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTAC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTAC
EST: gi|71863226|gb|DT012281.1|DT012281
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|110697228|gb|EE074032.1|EE074032
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
EST: gi|26267453|gb|CA818516.1|CA818516
EST:     TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTG                         TTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC
genomic: TTTCAGTGCTCTGGTCTGGACCCCTTCTGCTGATTGCTATCATAATTTTGgttagtgatc ... gattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccaggcctttgctttattatttccagaccctaaaccttcctttgattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCCGAGCTCAGGCATCGGGCACTACTTGCTAGAAACAAGCAGGATTAGTTTT
                                    ccttcctttgatttt  CT-rich tract
         tttgctttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgatcaaagctatttgcatatatgtttcatttttcacatgccgggcaccaggcctttgctttattatttccagaccctaaaccttcctttgattttgcagTTGAATACCCTCTTCTCTTTATGCCGACTACTAATTAAGTGGAAAAGAGCCGAGCTCAGGCATCGGGCACTACTTGCTAGAAACAAGCAGGATTAGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA