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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtatatatatattttttgtatcag

Basic information

species Glycine max
transcript GLYMA16G06850.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 10
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgt------cagatgaa-atgt-tgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtatatatatattttttgtatcag
||||| || || || || |||||||| || || || ||||| || ||||||||||| |||||| |||| || || ||  ||||||||||||||||||| |||      |  || |  || | |  |||||    | ||  |  |    || | |||   ||| |||  |  |||  |        | ||   |  | | |  ||||| || | ||||     |  |     |  |                   
CAATACGAGGGGTACAAGGATGACCCTACAGTGCCAGATGACTCAAACACCCCAACTTTTGCATCTGTCGTGCTTCGGGTACACAATGAAAGATGGGAGGgtatgtctctcatcagtatatatacacattagggttctggagaaggacaacattgat-tttcgttt--tcccttcagattgtctttcagtggaccataattcttcattttaactctgtaatattcatatcctgcag------------------

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 11
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgt-----------cagatga-aatgt-tgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtat---atatatattttttgtatcag
||||| || ||||| || |||||||| || || || ||||| || || |||||||| |||||| |||||||||| ||  |||||||||||||||||||||||           || |||| | | | || |||| |  |   | |||   ||| | | ||||  | | |    | | |||  | ||   | |  |    | |  |    |||| |   | |  |  ||  |  ||   |   ||||  ||  |||| |    
CAATACGATGGCTACAAGGATGACCCTACAGTGCCAGATGACTCGAATACCCCAACTTTTGCATCTGTTGTTCTTCGGGTACACAATGAAAGATGGGAAGgtatatcttcacccacatgacagtatctgtacatattgtagttgaaatggatata-attgaaa-tacttgctctctgtttttttcattcaatgtgccttttc--tcaaccataatatctttactttctgtatcaaccttctaatattcatgctttgcag---

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcag-atgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatt-----tctttggtgcaaaaattaggaaaat---acagtagttcatat-tcattctggtgcctaaaagaagtata-tatatattttttg-tatcag---------------------
|||||||| ||||| || |||||||| || || || ||||| || |||||||| || |||||| ||||||| ||| |  ||||||| ||||||||||| ||| |  || |   | ||| |  || || ||    |      |   ||| ||  | | |||||      ||  |  |   | ||   |  || |   ||  |   ||||||  || | |  | | |   |  | |  | | | |||| |||| |   |                      
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctccc----aatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 11
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 11
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtatatatatattttttgtatcag
||||| ||||| || | |||||||||||| || |||||    || || |||||||| |||||| || |  ||||||| ||||||||||||||||||||||||  ||  |  | || |  | ||  | | |  ||   ||      |  |   | ||| |  |  || |  ||||   ||   ||  | |  |   | | |||                                            
CAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaatttatttataaattattgcatttaatttatcctctttataaaatacttca-ctgtttggaggcaagttttctaaacctcccatcagt-aaatt--------------------------------------------

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|6566164|gb|AW233801.1|AW233801
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|15815763|gb|BI788038.1|BI788038
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|7925329|gb|AW831416.1|AW831416
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|16343150|gb|BI968745.1|BI968745
EST:     ATTTGCAACTGTTGTTCTGCGAATANNNAATGAAAGATGGGAAG                         GTGTTCCNNNCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: ATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|58023690|gb|CX710431.1|CX710431
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|16346631|gb|BI972226.1|BI972226
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|192310376|gb|FK002256.1|FK002256
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|16346044|gb|BI971639.1|BI971639
EST:     GTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: GTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|15661712|gb|BI699083.1|BI699083
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|58020056|gb|CX706798.1|CX706798
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|151395248|gb|EV265119.1|EV265119
EST:     CCAACATTTTGCAACTGTTGTTCCGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCAACA-TTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|17519559|gb|BM188601.1|BM188601
EST:     CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... tttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtatatatatattttttgtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG