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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctcttttactgttaatctggtagatatgagcaggaaaactctactagatttatcactcataagcatcaaatttagtcatgctaggaatcagttc...

Basic information

species Vitis vinifera
transcript Vv15s0048g02730.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G132519_T01 (Zea mays), 5'ss of exon 5
TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctcttttactgttaatctggtagatatgagcaggaaaactctactagatttatcactcataagcatcaa--atttagtcatgctaggaatcagttc-------------
||||  ||||| | |  || ||||||||  | |||||||| ||||  || |   | ||| ||||| | ||  |||||||||| |||||||||||||||||||| || || || |||  ||| ||| |  ||     |     || | |  ||  | | |   |  || | |  ||   | |||   | |    |  || |               
TTGCACAGAGAAGGGATGAGAAGAAGAAGAGGGTTGAAAAGCAAGAAAAAAGCAGATTAGAGAATTTAAAGAAAGCTGCAAAGGTTGGTGCTTTGCCAAGgttgttatccttcactagtaa-ctgctgcatcccctcctttcaattatg-tatgtctttttgtattaggaaggaaccttctagaattacagctacccaatatcttttgtatgcag

upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G132519_T02 (Zea mays), 5'ss of exon 5
-----------------TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctcttttactgttaatctggtagatatgagcaggaaaactctactagatttatcactcataagcatcaaatt--tagtcatgctaggaatcagttc-------------
                 ||||  ||||| | |  || ||||||||  | |||||||| ||||  || |   | ||| ||||| | ||  |||||||||| |||||||||||||||||||| || || || |||  ||| ||| |  ||     |     || | |  ||  | | |   |  || | |  ||  |  |||   | |    |  || |               
GCCTGGTGTTGATCCCTTTGCACAGAGAAGGGATGAGAAGAAGAAGAGGGTTGAAAAGCAAGAAAAAAGCAGATTAGAGAATTTAAAGAAAGCTGCAAAGgttggtgctttgccaaggttgttatccttcactagtaa-ctgctgcatcccctcctttcaattatg-tatgtctttttgtattaggaaggaaccttctagaattacagctacccaatatcttttgtatgcag

upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G12440.2 (Glycine max), 5'ss of exon 5
TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgttt-------ttctcttttactgttaatctggtagatatg--agcaggaaaactctactagatttatcactcataagcatcaaatttagtcatgctaggaatcagttc
|||| || |||  || | | ||||||||  || |||||||||| | ||| ||||| ||||||||  | ||| ||||||||||| |||||||||| |||||||||       | || |||| |  |||| || | || | |   |||| |  ||   || | | ||      |||| || ||     | | |   ||| | | |      
TTGCCAAAAGAAAAGAAAATAAGAAGAATAGAATTGAAAAACAGGAGAAAAATCGATTACAGAACTTGAAAGAAGCTGCAAAATTTGGTGCTTTACCAAGgtttgccacgttccttttttccaattaaccttgaagcttttgcagcatgggaatcatatttgtttc--tgttcatcagaatatccatcattg--gcttgtagtt-----

upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G23700.1 (Glycine max), 5'ss of exon 5
TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttc--------tcttttactgttaatctggtagatatgagcaggaaaactctactagatttatcactcataagcatcaaatttagtcatgctaggaatcagttc
|||| || ||   || | | ||||||||  || |||||||||| | ||| ||||| ||||||||  | ||| ||||||||||| |||||||||| ||||||||| ||        | |||| |  |||| || | || | |  |||| |       |    |||| |  ||  | | ||  | ||| | ||||  | |   | || | 
TTGCCAAAAGGAAAGAAAATAAGAAGAATAGAATTGAAAAACAGGAGAAAAATCGATTACAGAACTTGAAAGAAGCTGCAAAATTTGGTGCTTTACCAAGgtttgtcaagtacctttttttccaattaaccttgaagctttt-gcagcatggg---atcctatttgtttctgttcatcagaatattca-tcat--tggcttttagct-

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|110690893|gb|EE068371.1|EE068371
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|26257434|gb|CA808497.1|CA808497
EST:     AATCGGTTACAGAATCTCAAGCAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|71878852|gb|DT027907.1|DT027907
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|30252208|gb|CB969759.1|CB969759
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|110409092|gb|EC974748.1|EC974748
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|30251454|gb|CB969187.1|CB969187
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|110715690|gb|EE094027.1|EE094027
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|71878364|gb|DT027419.1|DT027419
EST:     AATCGGTTACAGAATCTCACACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGA
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGA
EST: gi|27578726|gb|CB001421.1|CB001421
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|71880010|gb|DT029065.1|DT029065
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|110367133|gb|EC931058.1|EC931058
EST:     AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
EST: gi|26257329|gb|CA808392.1|CA808392
EST:     AATCGGTTACAGAATCTCAAGCAAGCTGCAAAAGTTGGTGCTTTGCCAAG                         CCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC
genomic: AATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctct ... ttttccccagCCACATTCAACTTGCTGCCACAGCCTTACCTATTACTGGAACCCAAACTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTAAGAGACGAGCAGAAAAGAAGAAACGAGTTGAAAAACAAGGGAAGAATCGGTTACAGAATCTCAAACAAGCTGCAAAAGTTGGTGCTTTGCCAAGgtttttctcttttactgttaatctggtagatatgagcaggaaaactctactagatttatcactcataagcatcaaatttagtcatgctaggaatcagttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaaa