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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttcttagacagctttgacctcatttaggaactggcttctattagtttatttctctttgttatgcataagtaatgataatagtgtatgcttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTGCTGACCTTACAGGTTTCCTGCCTCTCTCAAAAATTAAAGTCCTTGCAAG

Basic information

species Vitis vinifera
transcript Vv04s0044g01940.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G21960.2 (Glycine max), 3'ss of exon 3
ggtttcttagacagctttgacctcatttaggaact---ggcttctattagtttattt---ctctttgttatgcataagtaatgataatagtgtatgctt-cttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTGCTGACCTTACAGGTTTCCTGCCTCTCTCAAAAATTAAAGTCCTTGCAAG
        | | |  |  | | |   ||||  ||      | | | | ||   | ||    | || ||  | ||| |  | | | || ||| | |  || | |||||| ||||||||||| |||||||||||| |||||||||| ||||||||| | ||||||   ||| ||||  |||||||  | ||||| ||||| ||||| ||
-------aacaaaattcggtcttttattagagaccttaaacatatttaagccaaatttaattgttagtagttcatgaaaattaacaacagtatgtcttttcgtgcagTTTTTGGTTATGAACCACATTCAGTTTTGCCAATTGGAGTTGTTGCATTAGCTGACAACACATGTTTTATGCCTCTTCCTAAAATAAAAGTTCTTGCTAG

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G32790.1 (Glycine max), 3'ss of exon 3
ggtttcttagacagctttgacctcatttaggaactggcttctattagtttatttctctttgttatgcataagtaatgataatagtgtatgctt-cttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTGCTGACCTTACAGGTTTCCTGCCTCTCTCAAAAATTAAAGTCCTTGCAAG
  ||      ||| || |  |     | | |       || |||| || | ||  | || ||  | ||| | || | | || ||| | |  || | |||||| ||||||||||| |||||||||||| |||||||||| ||||||||  | ||||||   ||||||||  |||||||  | ||||| ||||| ||||| ||
-tttaagctaacatctctctctatggtgatggctcctattttatttgtattttattgttagtagttcatcaatattaacaacagtatgtcttttcatgcagTTTTTGGTTATGAACCACATTCAGTTTTGCCAATTGGAGTTGTTGCGTTAGCTGACAACACAGGTTTTATGCCTCTTCCTAAAATAAAAGTTCTTGCTAG
















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|110719781|gb|EE095207.1|EE095207
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|351031411|gb|FQ445436.1|FQ445436
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|351042865|gb|FQ451159.1|FQ451159
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCTATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCCCTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|349830416|gb|FQ420676.1|FQ420676
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|110410772|gb|EC976464.1|EC976464
EST:     TGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: TGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|110366687|gb|EC930603.1|EC930603
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|110718650|gb|EE095723.1|EE095723
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|110405821|gb|EC971375.1|EC971375
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|349810065|gb|FQ401511.1|FQ401511
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|349810606|gb|FQ402849.1|FQ402849
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|30131047|gb|CB916386.1|CB916386
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|156739053|gb|EV243166.1|EV243166
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
EST: gi|110719222|gb|EE096951.1|EE096951
EST:     GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATG                         TATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG
genomic: GACTCTATATGTGGAGGATATAAAAGCGTTCGACCCCAATCGTGCCTATGgtaaattcac ... cttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatttctctttgttatgcataagtaatgataatagtgtatgcttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTGCTGACCTTACAGGTTTCCTGCCTCTCTCAAAAATTAAAGTCCTTGCAAG
                                           tgcttctt  CT-rich tract
                      ataagtaatgataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttcttagacagctttgacctcatttaggaactggcttctattagtttatttctctttgttatgcataagtaatgataatagtgtatgcttcttgcagTATTTGGTTATGAGCCACATTCAGTTCTGCCAATTGGTGTTGTTGCACTTGCTGACCTTACAGGTTTCCTGCCTCTCTCAAAAATTAAAGTCCTTGCAAG

- - - - - - - - -tgacctc
- - - - - - - - - - - - - - - - - tggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg