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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattgggacctgggtttaacatgggaaaagcctgaaaggtaggtgaggaacagtccaacctgaggagctgaaacaggcatctttttttatttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG

Basic information

species Vitis vinifera
transcript Vv04s0044g01940.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G21960.3 (Glycine max), 3'ss of exon 5
ggattgggacctgggtttaacatgggaaaagcctga-aaggtaggtgaggaacagtccaacctg-aggagctgaaacaggcatctttt---tttatttg--ttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG-------------
       ||   || ||  | ||   |   | || |  |  |      |    | |   | ||  |       |      ||   ||     |||||||  || ||| ||||||| || || ||||| | ||||||||| |||||||| ||||||| ||||   ||| ||||||||||||||||||||||||||             
-------gaaaaggtttccaaataaaatgggtcttatgatatgaaactgctttaatttgatctatattcatacaggttaacaatattaagaattatttgctttctagATTGCCTTTCTTAAATCAAGGAGAGGATTTGTCCGCATAGCAATGGAGAAGGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAGGTATTTATTTCTT

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G21960.2 (Glycine max), 3'ss of exon 5
ggattgggacctgggtttaacatgggaaaagcctga-aaggtaggtgaggaacagtccaacctg-aggagctgaaacaggcatcttt---ttttatttg--ttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG
       ||   || ||  | ||   |   | || |  |  |      |    | |   | ||  |       |      ||   ||     |||||||  || ||| ||||||| || || ||||| | ||||||||| |||||||| ||||||| ||||   ||| ||||||||||||||||||||||||||
-------gaaaaggtttccaaataaaatgggtcttatgatatgaaactgctttaatttgatctatattcatacaggttaacaatattaagaattatttgctttctagATTGCCTTTCTTAAATCAAGGAGAGGATTTGTCCGCATAGCAATGGAGAAGGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAG

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G32790.1 (Glycine max), 3'ss of exon 5
---ggattgggacc---tgggtttaaca-tgggaaaagcctgaaaggtaggtgaggaacagtccaacctgaggagctgaaacaggcatctttttttatttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG
   || ||  ||     ||||| | ||| |  ||||   ||  |   ||  |||   | | ||  ||  |   | |   |  | | ||   ||  |     || ||| ||||||  || ||  ||||||  |||||||| |||||||| |||||||  |||   ||| ||||||||||||||||||||||||||
aagggtttcagataaaatgggtcttacaatatgaaacttctttatttta--tgaattatattcatacaggtttaacaatataaagaattaattgct-----ttctagATTGCCTATCTTAAAGCAAGAAGGGGATTTGTCCGCATAGCAATGGAGAAAGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAG

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G21970.1 (Glycine max), 3'ss of exon 5
--ggattgggacctgggtttaacatgggaaaagcctgaaaggtagg--tgaggaacagtccaacctgaggagctgaaacaggcatctttttttatttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG
   |||| |  |      | || |  |       | | | |  | |  |  |  | | | |||  | |   |    || ||      | ||     | |||||| ||||||| || |||  ||||| ||||||||| ||||||||  || | ||||| |  ||| | |||||||||||||||||||| |||
tcagattagatcagtttataaatactgtttgtatcggtaggaaatgtttatgatatatttcaaattcaaatgggttaatag----tatattaagaatattgtagATTGCCTTTCTTAAGCAAAGAAGAGGATTTGTCCGCATAGCATTGCAAATGGGCCTACCCCTTGTTCCAGTTTTCTGCTTTGGCCAG

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|110410772|gb|EC976464.1|EC976464
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
EST: gi|110718650|gb|EE095723.1|EE095723
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATACCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
EST: gi|110405821|gb|EC971375.1|EC971375
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
EST: gi|110715904|gb|EE094489.1|EE094489
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
EST: gi|30131047|gb|CB916386.1|CB916386
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
EST: gi|156739053|gb|EV243166.1|EV243166
EST:     TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAG                         GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG
genomic: TAGTGCCAGGTGGAGTGCAAGAGCCATGTCTTATGGAGCACGGTTGTGAGgttcaactct ... tttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaacagtccaacctgaggagctgaaacaggcatctttttttatttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG
                                   tctttttttatttgtt  CT-rich tract
                                  atctttttttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattgggacctgggtttaacatgggaaaagcctgaaaggtaggtgaggaacagtccaacctgaggagctgaaacaggcatctttttttatttgttgtagGTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
ggattgg
- - - - - - - - - - - -gggaaaa
- - - - - - - - - - - - - - - gcctgaa
- - - - - - - - - - - - - - - - - - - - - ggtgagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacag