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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcacaactcctccacctctcattttgttagcaacacgattatgtggttacctagaactctgatttgcaagtgaacatttatgaacttgttccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA

Basic information

species Vitis vinifera
transcript Vv07s0031g01970.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G32030.1 (Glycine max), 3'ss of exon 10
ctcacaactcctccacctctcattttgttagcaacacgattatgtggttacctagaactctgatttgcaagt--gaacattt--atgaa--cttgt-tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA
| | | | | | | | | | |||| | || || || | | |||| || || || || || ||||| | | |||||| || |||||||||||||| |||||||| ||||| ||| | ||||| ||||| || || ||||||||||| | ||||||||||| || |||||||| |
-----gctgcatgcgaatatggatgttgcaacggaat--ttatttcattttcttaaaatgttatttctttgtttgattatcctaattaatacttgtgtaaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGGCCAATGGGGATAGTCTGTTTCCAAACAGCAAAGGATA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 10
ctcacaactcctccacctctcattttgtta--gcaacacgatt-atgtggttacctagaactctgatttg--caagtgaacattt--atgaa--cttgt-tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA
|| || | || | | || |||||| ||| || | || || || | | |||| |||| ||| || || ||||| | | |||||| || |||||||||||||| |||||||| ||||| ||| | ||||| ||||| || || || ||| ||||| | ||||||||||| || |||||||| |
---------gctgcatgtgg-atatggatattgcaacagaatttatttcattttcttaaaatgttatttctttgtgtgatcatcctaattaatacttgtataaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGACCATTGGGAATAGTCTGTTTCCAAACAGCAAAGGATA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 10
ctcacaactcctccacctctcattttgttagcaacacgattatgtggttacctagaactctgatt-tgcaagtgaacatttatgaacttgttccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA
| |||| | | | | ||| || | |||| || || ||| || | ||| || | | | || |||||| || ||||||||||| ||||| ||||| ||||| || ||||| |||||||||| ||||| ||| ||| | || || ||||||| ||||||||||
----------------------gtatgtttgatctaatctcac-tggctatatc-aactatgcttctgcttgttataattgttggaaat-tgtgatttcagGAGGCGGAGAAGCATCTATCGGAGATGGTAGTGTCAAAAGCACTGATTGCAAAAATAGACAGACCATCTGGAATTGTGTGCTTCCAGATCGCAAAGGACA

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|110729885|gb|EE106329.1|EE106329
EST:     CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110364122|gb|EC927769.1|EC927769
EST:     CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110416190|gb|EC982152.1|EC982152
EST:     GCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: GCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110381624|gb|EC934958.1|EC934958
EST:     CGAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCAGAT--GGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110387763|gb|EC952457.1|EC952457
EST:     CGAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCAGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|351012778|gb|FQ430341.1|FQ430341
EST:     CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110684729|gb|EE062340.1|EE062340
EST:     CGAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCAGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
EST: gi|110387558|gb|EC952238.1|EC952238
EST:     CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG                         GAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA
genomic: CAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGgtttgcttaa ... tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttacctagaactctgatttgcaagtgaacatttatgaacttgttccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA
            ctctgat  putative branch site (score: 4)
 ttccatctc  putative PPT
 aacatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcacaactcctccacctctcattttgttagcaacacgattatgtggttacctagaactctgatttgcaagtgaacatttatgaacttgttccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
ctcacaa
- - - - tcctcca
- - - - - - - -cctctca
- - - - - - - - - - - - - - - -caacacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaac