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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGATGGTGACTATGAACTTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttccttttattaagggtgtactcgaagaccacatggaaatggaaaaaggaacgcttcattcttttggcacttgaagggacaaatatggttgaca...

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA20G33380.1 (Glycine max), 5'ss of exon 14
GGAGATGGTGACTATGAACTTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttccttttattaagggtgtactcgaagaccacatggaaatggaaaaaggaacgcttcattcttttggcacttgaagggacaaatat--ggttgaca-
|| |||||||| |||||||||||||||||||| ||||||||||| |||||||   |||||||| | ||||||||   | |  ||   |   | |||   ||   || ||     |  | |  | ||   ||  || |  |   |  |  ||  | || |||    ||   | 
GGTGATGGTGATTATGAACTTGTCAAGGATGTCATATTTGATGACTACCTCCGGCAGCGAATAGCTAAGgtatgaaacttcatac--attttataccacaacttcaaatttgg-taaatactgaaaaagttggttttgctattatatacagttataattattaaatttgaac

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA10G34150.2 (Glycine max), 5'ss of exon 12
GGAGATGGTGACTATGAACTTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatg---cttccttttattaagggtgtactcgaagaccacatggaaatggaaaaaggaacgcttcattcttttggcacttgaagggacaaatatggttgaca
|| ||||| || |||||||||||||||||||| ||||||||||| |||||||   |||||||| | ||||||||   |||| |    || | |    |     | |        | |   ||||||  | | || | | || |   |  |      ||   |||   ||   
GGTGATGGCGATTATGAACTTGTCAAGGATGTCATATTTGATGACTACCTCCAGCAGCGAATAGCTAAGgtatgaaacttcatacattttatgccacaacttcaaatttggcaaatacttaaaaagtta-gttttactattataa-atgtagtttaacttttattcatgta-

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT5G58330.3 (Arabidopsis thaliana), 5'ss of exon 10
GGAGATGGTGACTATGAACTTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtat-gcttccttttattaagggtgtactcgaagaccacatggaaatggaaaaaggaacgcttcattcttttggcacttgaagggacaaatatggttgaca
|||||||| || |||||||||||||||||||||  | ||||||| ||||| | | | |||||  ||||||||| || | |||  |         |  ||         ||  ||||   | |||          ||    ||  || ||||      ||||| |  |   
GGAGATGGAGATTATGAACTTGTCAAGGATGTAGAAATTGATGACTACCTTCGCCAACGAATCGCCAAGgtatagccttcttagagattaatctttttcaggttttgtatctaaatactagaag----------tttaactgagacatgaa------aatattgcag---

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|34550508|gb|CF518726.1|CF518726
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|34550427|gb|CF518645.1|CF518645
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACANGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110725848|gb|EE102783.1|EE102783
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110429818|gb|EC996325.1|EC996325
EST:     CAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: CAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|18459084|gb|BM437351.1|BM437351
EST:     CCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: CCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|351040604|gb|FQ438148.1|FQ438148
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110381192|gb|EC946513.1|EC946513
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|28963316|gb|CB342349.1|CB342349
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|33402579|gb|CF208206.1|CF208206
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110367124|gb|EC931047.1|EC931047
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110392317|gb|EC957652.1|EC957652
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|351046814|gb|FQ454424.1|FQ454424
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|349811478|gb|FQ409474.1|FQ409474
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAAGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110423097|gb|EC989434.1|EC989434
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|32245213|gb|CD711032.1|CD711032
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|18458671|gb|BM436949.1|BM436949
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|110393853|gb|EC959389.1|EC959389
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
EST: gi|29785366|gb|CB342287.2|CB342287
EST:     TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAG                         ACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG
genomic: TTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttcc ... aattttgcagACAGAAGCTGAGTTGCTTGCTGAAAAGAGATGTGTGGCCCATCTTACAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGATGGTGACTATGAACTTGTCAAGGATGTAATATTTGATGAATACCTCCTCAAGCGAATAACCAAGgtatgcttccttttattaagggtgtactcgaagaccacatggaaatggaaaaaggaacgcttcattcttttggcacttgaagggacaaatatggttgaca

- - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggacaaa