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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagtttttaagtttttatttacgcacacagacaacacattcttttgtcagtcatttgactcccaactttacttaaatgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAAGTTCGGTTGAATCTTCATGGAATTGTATCTGTCGAATCTGCAACT

Basic information

species Glycine max
transcript GLYMA15G01750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtcagtttttaagtttttatttacgcacacagacaacacattcttttgtcagtcatttgactcccaactttacttaaatgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAAGTTCGGTTGAATCTTCATGGAATTGTATCTGTCGAATCTGCAACT
            ||   | |||    |       |||| |   ||   | |     ||  |||  ||  |   |   |    | | || ||||||| || ||||| ||  ||| |   || |  |||||  | |||||||||||| | ||||| || ||||||||||| ||||| ||||| ||||||
-----------gtttgatctttgccca-atgtcaagactatgtatgactgtagtgctc--ttgtttctaatggtggatctcctttttgtagATTGGTCCCTTCCAGTCATCAAAAGGCGAGAGGGCAAAGCTGAAAGTGAAAGTTAGATTGAACCTGCATGGAATTGTCTCTGTTGAATCAGCAACT
















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|208156881|gb|GD952039.1|GD952039
EST:     AGATCAGCACATATACT                         ATTGGACCTTTCCAAGTCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAA
genomic: AGATCAGCACATATACTgtaagtcagt ... atgtatgcagATTGGACCTTTCCAA-TCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAA
EST: gi|207797328|gb|GD767990.1|GD767990
EST:     ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACT                         ATTAGGAACCTTTCCAATCTACAATAACTGAAAAA
genomic: ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACTgtaagtcagt ... atgtatgcagATT-GGA-CCTTTCCAATCTACAATAACTGAAAAA
EST: gi|208332516|gb|GE126569.1|GE126569
EST:     ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACT                         ATTGGACCTTTCCAANCTACAATAACT
genomic: ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACTgtaagtcagt ... atgtatgcagATTGGACCTTTCCAATCTACAATAACT
EST: gi|208254937|gb|GE056901.1|GE056901
EST:     ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACT                         ATTGGACCTTTCCAATCTACAATAACTGAAAAAG
genomic: ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACTgtaagtcagt ... atgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAG
EST: gi|19269982|gb|BM886238.1|BM886238
EST:     ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACT                         ATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAA
genomic: ATGATGATGTGAGTGAATTGCAAACACCTGCAAAGATCAGCACATATACTgtaagtcagt ... atgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaacacattcttttgtcagtcatttgactcccaactttacttaaatgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAAGTTCGGTTGAATCTTCATGGAATTGTATCTGTCGAATCTGCAACT
                      atttgac  putative branch site (score: 4)
                                    tttacttaaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcagtttttaagtttttatttacgcacacagacaacacattcttttgtcagtcatttgactcccaactttacttaaatgtatgcagATTGGACCTTTCCAATCTACAATAACTGAAAAAGCAAAAGTTAAAGTGAAAGTTCGGTTGAATCTTCATGGAATTGTATCTGTCGAATCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA