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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcgaatagattctgtcttaagaacatgaatagataatattctttctattttcttgtaaaggaatactcagtataattttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGA

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 10
gtgatcgaatagattctgtcttaagaacatgaatagat--aatattctttctattttcttgtaaaggaatactcagtataattttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGA
|| ||   |       |     || ||  ||  |  |   |||||   ||  | | |||||||    | |  |  ||    || | |  ||||||| |||||  |||||||||||||| |||| || || |||||||||||  | |||||    || ||||||||||| |||||||||||||| || || |
gtcattttaggatcattactagaataatctgcctgaactgaatatatctttaactctcttgtatgatattggt--gttatcttgttaatagGTCCCTGACTTCTTAAATGCTAGAATTGATGGTTTGCCAGTCAAAGAGGTGGTTAAGGATCATAAGTGGTTGGAGGAAGAGTTCACTGAAAAGGTTCAAA
















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:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|34550427|gb|CF518645.1|CF518645
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|110725848|gb|EE102783.1|EE102783
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|30137894|gb|CB923232.1|CB923232
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|351040604|gb|FQ438148.1|FQ438148
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|110381192|gb|EC946513.1|EC946513
EST:     GTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: GTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|28963316|gb|CB342349.1|CB342349
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGGCCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|110367124|gb|EC931047.1|EC931047
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|110392317|gb|EC957652.1|EC957652
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|351046814|gb|FQ454424.1|FQ454424
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|349811478|gb|FQ409474.1|FQ409474
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|18458011|gb|BM436289.1|BM436289
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG                         GTCCCAGACTTTCTAAACGCTAGAATTAATGGCTTGCCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
EST: gi|29785366|gb|CB342287.2|CB342287
EST:     ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGGCCACTCAG                         GTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC
genomic: ATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaat ... ttttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataatattctttctattttcttgtaaaggaatactcagtataattttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGA
                                             ttttcatc  CT-rich tract
     atattctttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcgaatagattctgtcttaagaacatgaatagataatattctttctattttcttgtaaaggaatactcagtataattttcatcagGTCCCAGACTTTCTAAATGCTAGAATTAATGGCTTACCCGTCAAAGAGGTCATCAAGGACATCAAATGGTTGGAGGAGGAGTTCACTGAAAAAGTCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG