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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaagcgcttcaacatttttcttatggtctaattagagcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag

Basic information

species Vitis vinifera
transcript Vv12s0059g01400.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os09g05020.1 (Oryza sativa), 5'ss of exon 3
GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaagcgcttcaacatttttcttatggtctaattaga-gcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag
||||| ||||||||||| || || |||| ||||||||| || ||||||||||| || ||||          || || | |   || |    |||||| |  |||| |||| |   |     || ||| || |  | ||    |  | |        
GAGCCCTTTGTGAACATACCTGAAGATAGAATCCGTGAGGCTCTAAAAGTTGTGCTAGgta----------tttaaaaatgacctaagctactaatttgtcgcattgtttttcccc---cctgattagatatcaaattctttttgtag--------

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G43550.1 (Glycine max), 5'ss of exon 3
GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaataca-agcgcttcaacatttttcttatggtctaattagagcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag
|||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||      ||  ||| |   ||  || ||   |  | ||  | ||    |  ||  ||||||||||  ||    | ||||     |     ||| ||
GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTGgtatggtgtagttctttatttttaatcata-actgcagtttcaaca--actcatt--caattttgctagcaataac-ttttggtgatcaataatgcag

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G05400.1 (Glycine max), 5'ss of exon 3
GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaataca-agcgcttcaacatttttcttatggtctaattagagcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag
|||||||||||||||||||||||||| |||||||||||||| ||| |||||||||||||||  |   ||  ||| |   ||  ||| |   |  | ||  | ||    |  ||||  ||||||||  ||    | |||  |         ||| ||
GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTGgtatgatgtagttctttacttttaatctca-actgcagtttcaaca--actcattta--attttgctagcaataacttttggcgatcaaataatgcag

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|30256135|gb|CB971978.1|CB971978
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|110389980|gb|EC954860.1|EC954860
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|351015527|gb|FQ447356.1|FQ447356
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCGTCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|26258262|gb|CA809325.1|CA809325
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|26257485|gb|CA808548.1|CA808548
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|351045015|gb|FQ449269.1|FQ449269
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACCTCTGATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|71857429|gb|DT006484.1|DT006484
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|110379464|gb|EC944660.1|EC944660
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|30253155|gb|CB970706.1|CB970706
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCCCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|351022573|gb|FQ447095.1|FQ447095
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|351034099|gb|FQ448017.1|FQ448017
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|110362858|gb|EC926416.1|EC926416
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|29785487|gb|CB342539.2|CB342539
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAACCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|30253078|gb|CB970629.1|CB970629
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|30256204|gb|CB972047.1|CB972047
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
EST: gi|83275093|gb|DV939189.1|DV939189
EST:     TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG                         ATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG
genomic: TGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaag ... tgctatgtagATGTAAGGAATCATCCACTTCTAATCCATTGCAAAAGAGGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGgtaatacaagcgcttcaacatttttcttatggtctaattagagcatagtttgtttacaattttgcttacatctgcattttacctgtttgctatgtag

- - - - - - - - - - AGAGGA
- - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - -  TGAAGC