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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctcttcaaattattttttcccatttaatgttatggtacttataattaaaatgttaatgtccaaccatattaggtgtgttttatccaattgaatct...

Basic information

species Vitis vinifera
transcript Vv12s0034g01440.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G19840.1 (Glycine max), 5'ss of exon 3
CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctcttcaa-attattttttcccatttaatgtt----atggtacttataattaaaatgttaatgtccaac--catattaggtgtgttttatccaattgaatct
 |||||| || |||| ||||| || ||||| |||||||| |||||||| ||||||| ||| ||||||||||| || ||||| |  ||||||||||||||||| |    ||||    ||||| |   |  ||||| |     ||  || ||  |  || ||| ||   || | ||  || ||  |    |   |||   ||       
TCATAATGAACGAGGTGGAGACGTTAGTGTGAACCTTGATTGGAAAACTGGAATTGCAGCCAAGGATTGGGATTCGGTTGCTAAAAAGGAGAAGATTGAGgtaaatatttcattggtatttataatctattaatatgcctgataataatttcatctagaattttttggttctacgtcacatctgaccaggactataacat-------

upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 2
CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctcttcaaattattttttcccatttaatgt---tatggtacttataattaaaatgttaatgtccaaccatattaggtgtgttttatccaattgaatct
||||| ||||||||  |  || || | ||| |||||||| |||||||  ||||||| ||| ||||||||||| || ||||| || || |||||||||||||| | ||    | |        |    || ||| |   ||   ||    ||  || ||  | | |||   |||  || | | |  |   ||  | |  |    
CCATAGTCAAGGAGTTGTTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacc-catcaagggc-tgacatttactctaggt-

upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G05190.1 (Glycine max), 5'ss of exon 2
CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacc-----tcttcaaattattttttcccatttaatgt-tatggtacttataattaaaatgttaat-gtccaaccatattaggtgtgttttatccaattgaatct
   | | | ||  || ||||| || ||||| |||||||| |||||||| ||||||| ||| ||||||||||| || ||||| |  || || ||||||||||| |       | |      |||| ||   |  || || |   || |  ||  |  || ||| ||  | || | |||  |  |    ||| |  |  ||        
TAGTGAACGAGCTGGTGGAGACGTTAGTGTGAACCTTGATTGGAAAACTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAAAAAAGAAAAGATTGAGgtaattaaacatttcgtcggtattattaatctattgatatgcctgatgttttcatctagaatttttttagttctacctcacaaaagctgtatactataac-------

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|349808549|gb|FQ405693.1|FQ405693
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351026894|gb|FQ436547.1|FQ436547
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAAATTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|77587717|gb|DV223037.1|DV223037
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351016734|gb|FQ424161.1|FQ424161
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|77581489|gb|DV219683.1|DV219683
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGA
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGA
EST: gi|349826899|gb|FQ418990.1|FQ418990
EST:     GAATTGGAGCANAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351028478|gb|FQ444759.1|FQ444759
EST:     GAATTGGAGCANAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|110390944|gb|EC955893.1|EC955893
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351031396|gb|FQ445421.1|FQ445421
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCATTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351034240|gb|FQ448037.1|FQ448037
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351014680|gb|FQ437880.1|FQ437880
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAGGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|71877423|gb|DT026478.1|DT026478
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351029626|gb|FQ427466.1|FQ427466
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
EST: gi|351017782|gb|FQ436135.1|FQ436135
EST:     GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAG                         GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT
genomic: GAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctctt ... tttcctgtagGGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctcttcaaattattttttcccatttaatgttatggtacttataattaaaatgttaatgtccaaccatattaggtgtgttttatccaattgaatct

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa