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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcattcatttgagtaagagctaatagtagagttccagactgcaatatttttcaccacttctacaccaattgagtgaaagtatagttttgtgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCATCTAAAGGAATGTTTATTGACTCTTGCTATGCCCACTGCCAAACAGAACC

Basic information

species Glycine max
transcript GLYMA16G17120.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 11
gtcattcatttgagtaagagctaatagta--gagttccagactgcaatatttttcaccacttctac-accaattgagtgaaagtatagttttgtgatttt---cagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCATCTAAAGGAATGTTTATTGACTCTTGCTATGCCCACTGCCAAACAGAACC
    ||   |||  |   | ||    ||   | |||     |||||| |     ||   |||  |  || ||| |  |     | |  |||| |  | ||   |||  |||| |    | ||    || ||| | |  |   |   ||  || || || ||||||||||| ||  |||| |||||||||||||||||||| |||  
---cttggcttgtttcctacctgcccgttttgggtttt---ctgcaacaacaaccatgtctttgaggactaatcgtttttggtttttttttttttttctttctcagATTTCAGGGTGCAGTTTCTTAGTGCAATCAAAGGACTGATAGGCTCCCCCTCCAAAGGAATGTTCATAAACTCCTGCTATGCCCACTGCCAAACCGAAAT
















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|6724656|gb|AW309111.1|AW309111
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
EST: gi|10709246|gb|BF008970.1|BF008970
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCNAAAGGGCATTGATTGAGGTAGGA
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGA
EST: gi|11117924|gb|BF219517.1|BF219517
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
EST: gi|192309097|gb|FG999058.1|FG999058
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
EST: gi|9900786|gb|BE609754.1|BE609754
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCTAAAGGGCATTGAGTGAGGTAAGAGATTCTCCAT
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
EST: gi|10709182|gb|BF008906.1|BF008906
EST:     CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAG                         GCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT
genomic: CAAGGTTAATATGAGCAACTGCTCGCCTGATCAACTAAGTAAATTGCAAGgtgaacactt ... tgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttcaccacttctacaccaattgagtgaaagtatagttttgtgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCATCTAAAGGAATGTTTATTGACTCTTGCTATGCCCACTGCCAAACAGAACC
                                                ttttc  CT-rich tract
                                   tatagtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattcatttgagtaagagctaatagtagagttccagactgcaatatttttcaccacttctacaccaattgagtgaaagtatagttttgtgattttcagGCTTCAAGAGTGAATTCGAAAGGGCATTGAGTGAGGTAGGAGATTCTCCATCTAAAGGAATGTTTATTGACTCTTGCTATGCCCACTGCCAAACAGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- cattcat
- - - - - - - - - - - - - - - - - - -gactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga