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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct...

Basic information

species Vitis vinifera
transcript Vv05s0094g00750.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctcta--aactactttaagcagtta----aactttgcaaaacttttgaaatgaggaaatgatgggaggct
| | || || ||||| || ||||||||| | ||  || | || ||||| |||||||||||||| |||||||||||||| || ||||||||||| || ||||||||   |      |  ||  |  |||  | | ||        | |   |    ||| ||    | ||  |||||     |    |  |||| |  | | |    
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagt--tcgaa----

upper sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct
  | ||||| ||  | ||||||||||| || || ||  |||||||||| |||||||  ||||| |||||||| || || || ||||| || || |||||||||||            | ||     |   | || | |||     |||  ||  |||     ||| ||    | ||| |                     
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag------------agca----gagtttcttctttctcgggaactcaaa--agtcggtttttcca---ttcttgcag--------------------

upper sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct
  | ||||||||  | ||||||||||| || || ||  |||||||||| |||||||  ||||| |||||||| || || || ||||| || || |||||||||||  ||                 |   | || | |||     |||  ||  ||||    ||| | |  |||                          
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagccc--------------agagtttcttctttctcgggaactcaaa--agttcggtttttccattcttccag----------------------

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|110698119|gb|EE075769.1|EE075769
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|110726698|gb|EE102705.1|EE102705
EST:     CATGAGAACAA-TTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAAAAAATAATCCCTAACTCGGGTTCA
genomic: CATGAGA-CAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCA
EST: gi|110733087|gb|EE108942.1|EE108942
EST:     ACATGAGACAAATTGAGAAGA-AATTCAATATTTGATTGGATCANGAATG                         GATCCACGGACAGAGAATAGTCCCTACCTCGGG
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGG
EST: gi|351043725|gb|FQ431078.1|FQ431078
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCTCGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|110685559|gb|EE062395.1|EE062395
EST:     ACTTGAGACCAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAAAAGTCCCTACCTCGGGTTCATCTAAACTTCAATT
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCA-TT
EST: gi|110729625|gb|EE105773.1|EE105773
EST:     ACATGAGACAAATTGAAAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAATAATCCCTACCTCCGGGT
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTC-GGGT
EST: gi|351027088|gb|FQ439949.1|FQ439949
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCTCGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|37187700|gb|CF607053.1|CF607053
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|351027733|gb|FQ446900.1|FQ446900
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCTCGGACAGAGAAAAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|351027735|gb|FQ446902.1|FQ446902
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCTCGGACAGACAATAGTCCCTACCTCGAGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|351016617|gb|FQ424044.1|FQ424044
EST:     ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
EST: gi|26264569|gb|CA815632.1|CA815632
EST:     ACATGAGACAAATTGAGAAGACGATTCAATATTTGATTGGATCAGGAATG                         GATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttcct ... cattttatagGATCCACGGACAGAGAATAGTCCCTACCTCGGGTTCATCTACACTTCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaat