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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatgtgaactgcttagtatatgtctcatattcataaagagagttggcattgggctggcacttgttgggttttggcttggcttggttgtgcaatttggctgaactcttctgtgttttgttcag

Basic information

species Vitis vinifera
transcript Vv06s0004g03140.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G052630_T03 (Zea mays), 5'ss of exon 3
---------------------------------------------------CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatgtgaactgcttagtatatgtctcatattcataaagagagttggcattgggctggcacttgttgggttttggcttggcttggttgtgcaatttggctgaactcttctgtgttttgttcag
                                                   |||||||||||||||||| | || || || |||||||||||||||||  || | |    |   |   |  |  |  ||  | | |||           ||   || | | |      | |  | ||     || |  | |  || ||| |   |  |                    
AGTATATGTCTGGCGGTTTTATACTCATGCATTTTTGCCTTCTCTATGAAGCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACTgtcagtaccatt--ccattccgcttccgttgc-tgttc-----------tgttcttcgccagaagtacgataaggttccttctgacgcgttgctgaaatgtaatttcag-------------------

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G052630_T01 (Zea mays), 5'ss of exon 4
CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatgtgaactgcttagtatatgtctcatattcataaagagagttggcattgggctggcacttgttgggttttggcttggcttggttgtgcaatttggctgaactcttctgtgttttgttcag
|||||||||||||||||| | || || || |||||||||||||||||  || | |    |   |   |  |  |  ||  | | |||           ||   || | | |      | |  | ||     || |  | |  || ||| |   |  |                    
CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACTgtcagtaccatt--ccattccgcttccgttgc-tgttc-----------tgttcttcgccagaagtacgataaggttccttctgacgcgttgctgaaatgtaatttcag-------------------

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G45300.1 (Arabidopsis thaliana), 5'ss of exon 6
CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatgtgaactgcttagtatatgtctcatattcataaagagagttggcattgggctggcacttgttgggttttggcttggcttggttgtgcaatttggctgaactcttctgtgttttgtt-cag
|| |||||||| |||||||| || |||||||||||||||||||| ||||||||  ||| |    | |  |  |   || | | |||  | |  ||      |||        ||    |   |     |||| | |  | |||  |   ||  |  ||| ||   | ||| ||| |||
CTTATCAGTGGAGAGCATGTTGGTGCTCTTGCAATGAGTGAACCTAATGgtaagatatatatttttcggatcaagagtttgagatt-gtgagaaggaaacacatcaat---acatacatatagccgatgctttgttctgatgtata--ctgatttgactttt---tatttcgttacag

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|352772844|gb|FQ470459.1|FQ470459
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|71863207|gb|DT012262.1|DT012262
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCCGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|352764155|gb|FQ467725.1|FQ467725
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|22010794|gb|BQ795828.1|BQ795828
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCCGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|71862993|gb|DT012048.1|DT012048
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|352781928|gb|FQ469225.1|FQ469225
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|161711972|gb|FC060027.1|FC060027
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGT
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGT
EST: gi|352772398|gb|FQ469923.1|FQ469923
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|71862585|gb|DT011640.1|DT011640
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCCGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|110729869|gb|EE106297.1|EE106297
EST:     CTTATCAGTGGGGAGCATGTANGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATAGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
EST: gi|352778090|gb|FQ467143.1|FQ467143
EST:     CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG                         CTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG
genomic: CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatg ... ttttgttcagCTGGCTCTGATGTTGTTAGTATGAAGTGTAAAGCTGATCGTGTTGATGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATGgtaatttatgtgaactgcttagtatatgtctcatattcataaagagagttggcattgggctggcacttgttgggttttggcttggcttggttgtgcaatttggctgaactcttctgtgttttgttcag

- - - - -  GGAGCA
- - - - - - - - - -  GGAGCT