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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgtagtaggggcgcatctcaggcatttgttgttttggttaaatattttggaaatactc...

Basic information

species Vitis vinifera
transcript Vv14s0128g00100.t01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA10G29770.1 (Glycine max), 5'ss of exon 19
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgtagtaggggcgcatctcaggcatttgttgttttggttaaatattttggaaatactc------
 |||||||||| ||||| ||||||||||| |||||||||||| |||| ||   | |      ||| |  ||| | |||   | |   |     |  || | ||   ||  |    ||  || || ||    | ||       
ATATGGACAACAGGAACAATGGGAGAACTAAGCCCAgtaagtgccttgtaccatgtt-----aattttgaaattttggctgaattatgttatctaacatg-atagattactccatttggattttctgttcctcctacttttc

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA03G40000.1 (Glycine max), 5'ss of exon 18
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgta--gtaggggcgca-tctcaggcatttgttgttttggttaaatattttggaaatactc
|||||||| |||||||| ||||||||||| ||||| |||||| ||||  ||| ||  | || ||| ||||   |||  | ||  ||  |   |   |  | || ||   |         |  |  | ||||    | ||
GTATGGACGACTGGAACAATGGGAGAACTAAGCCCCgtaagtgcctt--attataccttatcaat-tgaatcttattatatattgtgtgaatgtgctgccgggtatgcatctagaatacttcacctgttgggctgattc

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA19G42530.1 (Glycine max), 5'ss of exon 18
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgta--gtaggggcgca-tctcaggcatttgttgttttggttaaatattttggaaatactc
|||||||| |||||||| ||||||||||| ||||| |||||| ||||  ||| ||  | || ||| ||||   |||  | ||  ||  |   |   |    || ||   |        |||  | ||| |   || |  
GTATGGACGACTGGAACAATGGGAGAACTAAGCCCGgtaagtgcctt--attataccttatcaat-tgaatcttattatatattgtgtgaatgtgctgctgggtatgcatctagaatattacctgtttggctgattcct

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA03G40000.2 (Glycine max), 5'ss of exon 18
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgta--gtaggggcgca-tctcaggcatttgttgttttggttaaatattttggaaatactc
|||||||| |||||||| ||||||||||| ||||| |||||| ||||  ||| ||  | || ||| ||||   |||  | ||  ||  |   |   |  | || ||   |         |  |  | ||||        
GTATGGACGACTGGAACAATGGGAGAACTAAgccccgtaagtgcctt--attataccttatcaat-tgaatcttattatatattgtgtgaatgtgctgccgggtatgcatctagaatacttcacctgttgggct-----

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: AT3G05190.1 (Arabidopsis thaliana), 5'ss of exon 18
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtat-gtaatgaatctgaaaagtatggtgtagtaggggcgcatctcag-gcatttgttgttttggttaaatattttggaaatactc
||||||||||| ||||| ||||||||||| ||||| |||||| |     | | | | |||     |    |||  ||  |  | | |     || || |  | ||    |    |  ||||| | |||| | | |   
GTATGGACAACAGGAACTATGGGAGAACTAAGCCCGgtaagtacagaacagtctctagtagcttgtgaataaaacatcct-caatcgttctccacctgaatgtataacattcactaattaaa-actttgaataaatgg

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|34362676|gb|CF404261.1|CF404261
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|110418692|gb|EC984856.1|EC984856
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|33409556|gb|CF215183.1|CF215183
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|22014273|gb|BQ799307.1|BQ799307
EST:     CCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: CCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|33402079|gb|CF207706.1|CF207706
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|110424723|gb|EC991093.1|EC991093
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
EST: gi|22014530|gb|BQ799564.1|BQ799564
EST:     GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA                         GTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA
genomic: GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttcct ... cttttgttagGTTGTCAAGATTGATGGGCGCCCTGTTGGTGATGGACAAGTAGGGCCAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGACAACTGGAACCATGGGAGAACTCAGCCCAgtaagttccttttattgtatgtaatgaatctgaaaagtatggtgtagtaggggcgcatctcaggcatttgttgttttggttaaatattttggaaatactc

- - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaata