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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcattatttctatcaatcgtttcttctaatgcttttgtgatttacccattctaaaaagagcagcatgatgatccatgtcaaaaccattttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAAAAAGAGGAGAGAAGAAGCCAAAGCTGCTGCAGCTGCCCGTGTTCAAGCC

Basic information

species Vitis vinifera
transcript Vv13s0019g01900.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcattatttctatcaatcgtttcttctaatgcttttgtgatttacccattctaaaaagagcagcatgatgatccatgtcaaaaccattttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAAAAAGAGGAGAGAAGAAGCCAAAGCTGCTGCAGCTGCCCGTGTTCAAGCC
|||||| |||||   || || | |   ||     |    |||| ||  |    |   || | ||  |   |  || | ||||                  |||||| || ||||||||||||||||| ||||| ||  | ||||| || || || || | |||||||||||| |||||||||||||||||  |  ||||||| 
gtaagt-attataaataccatttggacctaacttttgacttgttatc-atgtgtgtaaatatgaaaacttttttgcttcatggttg--------------cagAGATCTGAAGAAGCAGAGAGAGATTGCTGCAGCTGCGAAAGAGGATGATAAGAAAAAGAGAGAAGAAGCAAAAGCTGCTGCAGCTGCTAGGATTCAAGCT
















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|28967033|gb|CB346066.1|CB346066
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110697869|gb|EE075334.1|EE075334
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110366799|gb|EC930717.1|EC930717
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|71877473|gb|DT026528.1|DT026528
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|351029576|gb|FQ427416.1|FQ427416
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|351024603|gb|FQ433018.1|FQ433018
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|22015347|gb|BQ800381.1|BQ800381
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGNNNNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110418060|gb|EC984172.1|EC984172
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|77587550|gb|DV222939.1|DV222939
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110376394|gb|EC941458.1|EC941458
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110415144|gb|EC981021.1|EC981021
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|28967261|gb|CB346294.1|CB346294
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110417551|gb|EC983617.1|EC983617
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|110422056|gb|EC988368.1|EC988368
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA
EST: gi|30302283|gb|CB979077.1|CB979077
EST:     AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA                         AGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGNNNN
genomic: AGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGAgtaagtcatt ... ttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccattctaaaaagagcagcatgatgatccatgtcaaaaccattttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAAAAAGAGGAGAGAAGAAGCCAAAGCTGCTGCAGCTGCCCGTGTTCAAGCC
     ttctaaa  putative branch site (score: 2)
                                        ccatttttt  putative PPT
                                    aaaaccattttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcattatttctatcaatcgtttcttctaatgcttttgtgatttacccattctaaaaagagcagcatgatgatccatgtcaaaaccattttttaatcagAGAGCTCAAGAAGCAGAGAGAGATGGCTGCTGCAACCAAAGAAGAAGAAAAAAAGAGGAGAGAAGAAGCCAAAGCTGCTGCAGCTGCCCGTGTTCAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC