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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatcttgtgtctactacctcaaatgacttgtctgctgtgttttgaattctcttcatgtttctcttaattgtgagttttgtaacttcacttttca...

Basic information

species Vitis vinifera
transcript Vv06s0004g08220.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G31470.1 (Glycine max), 5'ss of exon 4
AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatcttgtgtctactacctcaaatgacttgtctgctgtgttttgaattctcttcatg------tttctcttaatt-gtgagttttgtaacttcacttttca------------------------------------------------------
|||||||||| |||||||||| ||  | ||||||||||| || || || || ||||| ||||||||||||||| || | |||||||||||||| |||||||  |||| |  || || | |||  | |           |  | | || ||| || |||   ||      |||| |||  || |     |  ||  |||   | || |                                                      
AGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATCGTAAAATTGAGTTCCCTTTGCCTGATAGACGTCAAAAGAGGCTTGTATTTCAGgcaagtc-ttatgggttttctatatgattcactggaaattttatattctgactt-tctgagtggcaaattttcgcttgttttgctgactcagtgccttttatattgaaaaaatttgtagtttattttcatctgctagctaacctcttgatggtttgatcag

upper sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G31450.1 (Glycine max), 5'ss of exon 4
AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatcttgtgtctactacctcaaatgacttgtctgctgtgttttgaattctcttcatgtttctctta-attgtgagttttgtaacttcacttttca----------------------------------------------------------------------------------------------
|||||||||| |||||||||| ||  | ||||||||||| || || || |||||||| ||||||||||||||| || | ||||||||||| || |||||||  ||||   || || ||| |   | | |||  || | | |  | |||||       | ||||||| |   | ||| ||  || ||   ||  | |||                                                                                                 
AGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATCGTAAGATTGAGTTCCCTTTGCCTGATAGACGTCAAAAGAGGCTCGTATTTCAGgcaagtc---ttatggctatt---ttatatgctttattttc-atattttgtcagtattccatgtttattgaacattttgtattctgagtctctaatttcagtttggtttgcagacttacaatggcttttatattgaacattttaaatagtttattttcagctgcttgctaacctattatttgatgttttgatcag

upper sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 4
-AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtc--------atcttgt---gtctact-----------acctcaaatgacttgtct-gctgtgttttgaattctcttcatgtttctctta-attgtgagttttgtaacttcacttttca-----------------------------------
 |||||||||  |||||||||| ||  | ||||||||||| || || || || ||||| ||||||||||||||| || | ||||||||||| || |||||||  ||||        || || |   || ||||           |     | ||||   | | | | |||||||||  |  ||   || ||| |||  |||  |  |||      |   ||||||                                   
GAGCAGACACCTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATCGTAAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatca

upper sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatcttgtgtctactacctcaaatgacttgtctgctgtgttttgaattctcttcatgtttctcttaattgtgagttttg-----taacttcacttttca---------------------------
 ||||||||||| || ||||| ||  | |||||||||||||| || || |||||||| |||||  | |||||| || | ||||||||||||||||| ||||| ||| |  |  |     |   || |||| ||| || |   | | | ||||  |     |||||| ||| ||  |  |||||||     || |||   || |                             
GGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATCGTAAGATTGAGTTCCCCCTTCCTGATAGACGTCAAAAGAGGCTTGTTTTCCAGgtaagttaattactacaagca--cttaaataactagt-taaagagatatgaaaccaa---atgttt-tctcaaaagaaagttttgactgatatcttagtttctgtcttattgattggtttttccttgtgtag

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|352764633|gb|FQ469708.1|FQ469708
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110408764|gb|EC974405.1|EC974405
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|37184209|gb|CF603563.1|CF603563
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|30298944|gb|CB975738.1|CB975738
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|33405877|gb|CF211504.1|CF211504
EST:     ATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: ATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|27583947|gb|CB006642.1|CB006642
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|30330039|gb|CD013301.1|CD013301
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|71888901|gb|DT037956.1|DT037956
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110361748|gb|EC925244.1|EC925244
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|30329505|gb|CD012767.1|CD012767
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110374067|gb|EC938575.1|EC938575
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110696113|gb|EE074898.1|EE074898
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|71870890|gb|DT019945.1|DT019945
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|46918879|gb|CN548208.1|CN548208
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110370231|gb|EC929168.1|EC929168
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110386625|gb|EC951239.1|EC951239
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110406828|gb|EC972414.1|EC972414
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110693522|gb|EE069829.1|EE069829
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|29782278|gb|CB347461.2|CB347461
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|71886692|gb|DT035747.1|DT035747
EST:     CTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: CTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|33407022|gb|CF212649.1|CF212649
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|32459662|gb|CD800836.1|CD800836
EST:     ATTGAATTCCCTTTGCCTGATCGCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: ATTGAATTCCCTTTGCCTGAT--CGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|30298889|gb|CB975683.1|CB975683
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|110413373|gb|EC979155.1|EC979155
EST:     AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
EST: gi|32250054|gb|CD715873.1|CD715873
EST:     AAAAGAGGCTTGTTTTTCAG                         GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT
genomic: AAAAGAGGCTTGTTTTTCAGgtgagtcatc ... ctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACCGAAAGATTGAATTCCCTTTGCCTGATCGAAGACAAAAGAGGCTTGTTTTTCAGgtgagtcatcttgtgtctactacctcaaatgacttgtctgctgtgttttgaattctcttcatgtttctcttaattgtgagttttgtaacttcacttttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG