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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgccgttttgtttatgtatgctgtatcataatatctattttatgttaattgttgtttactaattcctttgtacttctataccataattttctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAGCTTGCTGGTCAGATTGTTAAGATGAGCCAGCAAAAGTTTGCTTCAAATG

Basic information

species Glycine max
transcript GLYMA10G35290.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35290.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 8
atgccgttttgtttatgtatgctgtatcataatatctattttatgttaattgttgtttactaattcctttgtacttctataccataattttctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAGCTTGCTGGTCAGATTGTTAAGATGAGCCAGCAAAAGTTTGCTTCAAATG
       |  | || || | |||  ||     | |||  || |||  ||| |      ||| ||        |  |  || |     ||| |    |||||||||  |  ||||||||||||| ||||||||| |    |||||||  ||||||||||| |||||||| |||||||| ||||||||||||||||| ||||
------gtaagattctg-aagcttaattgacgtttctgcttcatgaaaatggacac--actgat------aaagattaatcctg---tttccggctgtagCATATCATACAACATGGTAAACCTCATGAACGGTCAGAAATTATCAATAAGCTTGCTGGACAGATTGTGAAGATGAGTCAGCAAAAGTTTGCTTCTAATG

upper sequence: GLYMA10G35290.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04640.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------------------------------------------------atgccgttttgtttatgtatgctgtatcataatatctattttatgttaattgt----tgtttactaattcctttgtacttcta--taccataattttctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAGCTTGCTGGTCAGATTGTTAAGATGAGCCAGCAAAAGTTTGCTTCAAATG
                                                                                         | || ||||| | || | || | |||||| ||     | |||| |||  | |    | |||  || ||| ||||| |    |  | |  |  ||| |||   |||||| |  || || ||||||| ||||| |||||  || | ||||||||||||||||| || || || || |||||||| ||||| ||||||||||| ||||
gtacttttactaataaattttttgtttattttcttgttagatttcatgcttgaattccctttctctggtacttgtttcttttctgacttttcccttttgatgatctctgttttatcattattgtgttattattttacctataattttttttttacttcatttgtcccctgaggttcgttcctttgcttgtttagCATGTCTTGCAATATGGTAAGCCACACGAACGATCTGCTATTATCAGCAAGCTTGCAGGACAAATAGTAAAGATGAGTCAGCAGAAGTTTGCTTCTAATG
















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|213590609|gb|DB973340.1|DB973340
EST:     GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
genomic: GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
EST: gi|21888591|gb|BQ741804.1|BQ741804
EST:     AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAG                         CATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
genomic: AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAGgtatgtagct ... tctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
EST: gi|26057513|gb|CA800427.1|CA800427
EST:     GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
genomic: GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
EST: gi|6914723|gb|AW396253.1|AW396253
EST:     GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
genomic: GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
EST: gi|254348286|gb|GR851965.1|GR851965
EST:     AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAG                         CATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
genomic: AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAGgtatgtagct ... tctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
EST: gi|254330699|gb|GR841964.1|GR841964
EST:     AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAG                         CATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
genomic: AATCTGTCAGCACTTTAGCACAGGATCAATATGGAAATTATGTTATTCAGgtatgtagct ... tctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAG
EST: gi|21889642|gb|BQ742855.1|BQ742855
EST:     GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT
genomic: GTGCAATAATGAAATGTGTACGTGATCAAAATGGAAACCATGTTATTCAGAAGTGTATAGAGTGTGTCCCTCAAGATAAAATTCAGTTTATTGTTTCATCCTTTTATGGGCAAGTTGTTGCACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattgttgtttactaattcctttgtacttctataccataattttctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAGCTTGCTGGTCAGATTGTTAAGATGAGCCAGCAAAAGTTTGCTTCAAATG
            tactaat  putative branch site (score: 1)
                                          ttttcttt  putative PPT
                                tataccataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgccgttttgtttatgtatgctgtatcataatatctattttatgttaattgttgtttactaattcctttgtacttctataccataattttctttggtagCATATTGTGGAACATGGTAAACCACATGAACGGACTACCATTATCAGCAAGCTTGCTGGTCAGATTGTTAAGATGAGCCAGCAAAAGTTTGCTTCAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
-tgccgtt
- - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt