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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctctatatattgagtgatcaaattgttctgatgcttgcacatagctcctagtacatatgtggaggggaaaggatataacatttgcttttgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTCGTGGTGCTCATGATTGG

Basic information

species Vitis vinifera
transcript Vv05s0077g01190.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01190.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G15260.1 (Glycine max), 3'ss of exon 5
tgctctatatattgagtgatcaaattgttctgatgcttgcacatagctcctagt--acatatgtggagggga-aaggatataacatttgcttttgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTCGTGGTGCTCATGATTGG
   | | |||  | | || | |  ||  | |  |||       ||    | | |   | ||| |  |||  | | | |  | | |  | || |||  | |||||| | || |||||| |||||||||||||||| ||||| |||||||| |||||||| |||||||| |||
--gtgtttattctaaatggttattttcctgtattgcacaattttaaacgcaaatttccctatttataggacatatgaaccttaaagattctgttgaat-gcagGAGTGGCTGCAGGATTGTATTCAGGTCTCACATATGGGCTAAAGGAAGCTCGTGGAGCTCATGACTGG
















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|110385931|gb|EC950491.1|EC950491
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|30136712|gb|CB922050.1|CB922050
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|110395118|gb|EC960682.1|EC960682
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|30134613|gb|CB919951.1|CB919951
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|110391064|gb|EC956018.1|EC956018
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|32268099|gb|CD717258.1|CD717258
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|110364592|gb|EC927963.1|EC927963
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|30129205|gb|CB914544.1|CB914544
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|110402148|gb|EC968786.1|EC968786
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
EST: gi|110401165|gb|EC967764.1|EC967764
EST:     GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGG                         GACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC
genomic: GTGAAGAGCACAGGAAAAGAATCTCTTCAATGGGgtaattaagt ... tgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcctagtacatatgtggaggggaaaggatataacatttgcttttgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTCGTGGTGCTCATGATTGG
                             atataac  putative branch site (score: 3)
                                     tttgctttt  CT-rich tract
                             atataacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctctatatattgagtgatcaaattgttctgatgcttgcacatagctcctagtacatatgtggaggggaaaggatataacatttgcttttgtgtcgcagGACTAGCAGCAGGAATGTATTCAGGTCTCACCTATGGTCTAAAGGAGGCTCGTGGTGCTCATGATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - atcaaat
- - - - - - - - - - - - - - tctgatg
- - - - - - - - - - - - - - - - - -cttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggat