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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctcccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgcttgtatccattttaatgtctctttacattatgctattacag

Basic information

species Vitis vinifera
transcript Vv09s0002g00380.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 5'ss of exon 10
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctcccaaagtcaatatgtaggctgttccaattttcaagt--agattaaatgcttgtatccattttaatgtctctttacattatgctattacag
|||||| ||||| ||||||||||| || || ||||| || |||||||||||||||||| |  |||| |||||||| |||||||||||||| ||||| ||||||||||  ||  | ||| |||    |       |  |||  |          |||  |  ||   ||| | ||   || | || || ||      |||| || ||   |        
GAACTTGATTGAGGCAATGCCAACGTCACCAATTTTCGTTGGGAACAAGGCAAAGAGGCTTCTGGAAAGAGCTGTTTGGAATGATACTTCCTTTCTGGCAgtaagttcagattctgatagtgagaattatctcattcatacatg---------aatccttgagctaagacttaaaaattat-tcaatattttcaaatcttcacctttaac--------

upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G153722_T01 (Zea mays), 5'ss of exon 10
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctc-ccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgcttgtatccattttaatgtctctttacattatgctattacag
||||||||||||||||||||||||||| || |||||||| ||||||||||||||| || |  |||| |||||||| ||||| ||||| ||||| || || |||||||| | | |   || |  | |||  |||||   ||| | |   ||       || ||     ||      ||| |     | || |    |||| |                
GAACTTAATTGAAGCAATGCCAACTTCACCGATTTTTGTTGGGAACAAGGCAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagttt-gcatcaatttatccttctcatcaaagcttataggaaa--tgcagtggcttccagagctatcttcaacttcttcttttgttcaacaatcttcagc--------------

upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA07G05100.1 (Glycine max), 5'ss of exon 11
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctcccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgc----ttgtatccattttaatgtctctttacattatgctattacag
|||||||||||||||||||||||||||||| ||||| ||||| ||||| || || ||  |||| |||||||||||||||||||| |||  ||||||||| |||||| || |       ||||    ||          ||  |      ||    |||||  | | | |  |  |    || | | ||| |     |   | |   ||   ||  | |||
GAACTTAATTGAAGCAATGCCAACTTCTCCTATTTTCGTGGGAAACAAAGCGAAAAGATTGTTAGAGAGAGCTGTCTGGAATGACACTGGTTTTCTTGCTgtaagtcttaactttatctgtgacattctttcttctcttaactgtctcctttttcttttcttgcaaaatgcacaccatattatgttcatctcc-catgaatctgttttcctcttgtgcag

upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA16G01590.1 (Glycine max), 5'ss of exon 12
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttg----ctcccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgcttgtatccattttaatgtct-ctttacattatgctattacag----------
|||||||||||||||||||||||||||||| ||||| ||||| ||||| || ||  |  |||| |||||||||||||||||||| |||  ||||||||| |||| | |  ||||    | ||| |    || ||       |  |||   || |||   |||           || |||   |   ||| || |||||    | |||| |  || ||              
GAACTTAATTGAAGCAATGCCAACTTCTCCTATTTTCGTGGGAAACAAAGCTAAACGATTGTTAGAGAGAGCTGTCTGGAATGACACTGGTTTTCTTGCTgtaaatctcaaaactttatatgtggcattcttccttctcttaactgtctccttttcttgtttcttttcttgcaaagtgcacatcatcatctttatgtccatctcacataaatctgttttcctcttgtgcag

upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT3G14270.1 (Arabidopsis thaliana), 5'ss of exon 11
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctcccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgcttgtatccattttaatgtctctttacattatgctattacag
 ||||| ||||||||||||||||||||||||||||| || || ||||| |||||  |  ||||||| |||||||||||||| |||||| ||||||||||||| ||||||       ||| |  |||     ||  || |   ||  ||   | | | ||  |  || || | |     || | || ||  |   | ||| ||              
AAACTTGATTGAAGCAATGCCAACTTCTCCCATTTTCGTCGGTAACAAAGCAAAACGATTGTTGGAAAGAGCTGTCTGGAACGATACTGCTTTTCTTGCAgtgagtttt-------attcttctgc-----aaaccatt---tactcttcactactctttgaaaaggtttattagcaataactatattttt-cgtgtttgcag-------------

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|34547915|gb|CF516147.1|CF516147
EST:     GAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: GAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349814824|gb|FQ410047.1|FQ410047
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATCCTTCTTTTCTTGCA                         TCTGTTGATGTGA
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGA
EST: gi|351023163|gb|FQ432546.1|FQ432546
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|351037296|gb|FQ457129.1|FQ457129
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349813704|gb|FQ413938.1|FQ413938
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349813666|gb|FQ413900.1|FQ413900
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|30320712|gb|CD003974.1|CD003974
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349823260|gb|FQ400239.1|FQ400239
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATTTGATGGATTACTCAGTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|30128919|gb|CB914258.1|CB914258
EST:     CAAAGAGNGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGGAT-ACTCATTTACTGGT-GGGGTGGACGAGGAGA
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGG-ATTACTCATT-ACTGGTTGGGGTGGACGAGGAGA
EST: gi|349821544|gb|FQ408103.1|FQ408103
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|352791391|gb|FQ480970.1|FQ480970
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACCAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349814303|gb|FQ398743.1|FQ398743
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGGTGGACGAGGAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGG-TGGACGAGGAG
EST: gi|110364315|gb|EC923856.1|EC923856
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349814433|gb|FQ398873.1|FQ398873
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAA
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTC-TGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAA
EST: gi|30321214|gb|CD004476.1|CD004476
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG
EST: gi|349815793|gb|FQ400949.1|FQ400949
EST:     CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCA                         TCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAA
genomic: CAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttg ... gctattacagTCTGTTGATGTGATGGATTACTCATTACTGGTTGGGGTGGACGAGGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTTAATTGAAGCAATGCCAACTTCTCCCATTTTTGTGGGGAACAAGGCAAAGAGGGTGTTGGAGAGAGCTGTCTGGAATGATACTTCTTTTCTTGCAgtaagttttgaaaccgattgtgttgctcccaaagtcaatatgtaggctgttccaattttcaagtagattaaatgcttgtatccattttaatgtctctttacattatgctattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT