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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgacattactggacgggttatgttttatgatgattctcgaaatgctataaatggttatgccttttttctaacattcactttatctgacttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTATTAACTGGTTAACTGGAAAGTTATGTTCAAAACTCTTAAATTTCCATTC

Basic information

species Vitis vinifera
transcript Vv12s0035g01870.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 9
--tgctgacattactggacgggttatgttttatgatgattctcgaaatgctataaatggttatgccttttttctaaca--ttcactttatctgacttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTATTAACTGGTTAACTGGAAAGTTATGTTCAAAACTCTTAA-ATTTCCATTC-
    |||| |||  | ||      || ||||| |   ||      |    | |   | || |  | ||     |  ||  || |  | || |   |   || |||| ||||| ||||||||||||| ||| |||||||| ||||| ||||||     |  || | |  |   |  | || |||  | || |    |  |   ||  
tggtctgagatttgttgag----cattttttaagtacatatatatatgtgtgtgtgttgtaagccattgcagatgccaagttgatataatatatttgtgtgcagGGTTGGACGATGTCAGAATCACATCTAAATCCTGGTCGAGCACGGCTTCATCCAGTTGATAA--TAATAGATGATATTCTCAGCTTTCGGCAGCTGGGTTTT

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 12
tgctgacattactggacgggttatgttttatgatgattctcgaaatgctataaatggttatgccttttttctaacattcactttatctgacttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTATTAACTGGTTAACTGGAAAGTTATGTTCAAAACTCTTAAATTTCCATTC--
        | ||| |  | |  |  | |||| ||  || |  |  |  | |||  |  | ||| | |     || ||||  |||          |  ||||| |||| |||||||||||| || |||||||||||||| ||| || || | | |  ||    |  ||  ||| |   ||     |    | |   |||    
-------gtaacttgg-gagaaacctgttat-atcctttttaagttatt-taatcgagtgtgcatctg----aaaattccattt----------tgatagGGTTGGAGAATGTCAGAATCTCTGCTTAATCCTGGCCGGGCTAGG-TTATGTCATGTGAAGGAG-GGGGAGTAAACATCGCCTGTTGAGACTGGTCATCGAC
















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|30304025|gb|CB980819.1|CB980819
EST:     AAATGGTCTCCACTTCATATGGCCTTTTCAAGAGTAAAGCTGCTGAACAG                         GANTGGACAATGTCAGAATCACTTCTTA
genomic: AAATGGTCTCCACTTCGTATGGCCTTTTCAAGAGTAAAGCTGCTGAACAGgtgagtagaa ... cttcttgtagGGGTGGACAATGTCAGAATCACTTCTTA
EST: gi|110711704|gb|EE088489.1|EE088489
EST:     AAATGGTCTCCACTTCGTATGGCCTTTTCAAGAGTAAAGCTGCTGAACAG                         GGGTGGACNATGTCAAAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTA
genomic: AAATGGTCTCCACTTCGTATGGCCTTTTCAAGAGTAAAGCTGCTGAACAGgtgagtagaa ... cttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTA
EST: gi|161717211|gb|FC067217.1|FC067217
EST:     AAATGGTCTCCACTTCGTATGGCCTTTTCAAGAGTAAAGCTGCTGAACAG                         GGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTA
genomic: AAATGGTCTCCACTTCGTATGGCCTTTTCAAGAGTAAAGCTGCTGAACAGgtgagtagaa ... cttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctataaatggttatgccttttttctaacattcactttatctgacttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTATTAACTGGTTAACTGGAAAGTTATGTTCAAAACTCTTAAATTTCCATTC
                                             cttcttgt  CT-rich tract
                   ttttttctaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgacattactggacgggttatgttttatgatgattctcgaaatgctataaatggttatgccttttttctaacattcactttatctgacttcttgtagGGGTGGACAATGTCAGAATCACTTCTTAATCCTGGCCGAGCTCGGCTTGTATTAACTGGTTAACTGGAAAGTTATGTTCAAAACTCTTAAATTTCCATTC

- ctgacat
- - - - - - - - - - - - - - - - - - - - -gaaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcac