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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaataattggctttcacttagcaacttaattgtttaattttgggattgactcgctgacagatattttcttttatgttgtttatatag

Basic information

species Glycine max
transcript GLYMA01G40210.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G40210.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ23242 (Selaginella moellendorffii), 5'ss of exon 2
CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaataattggctttcacttagcaacttaattgtttaattttgggattgactcgctgacagatattttcttttatgttgtttatatag
||| ||||||||||| || |||||||||||  |||||||||| || || ||||| ||||| |||||||| ||     | ||||||||||| | | ||  || |    | ||   ||   || |   | |   ||||  || |                                  
CCTCTTCTTCAAGCAAGAGATGGAGTTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCTgtaagttcca-agttctctcttttctcgctctttcgctgatggttatc--gattttctag----------------------------------

upper sequence: GLYMA01G40210.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ25249 (Selaginella moellendorffii), 5'ss of exon 2
CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaataattggctttcacttagcaacttaattgtttaattttgggattgactcgctgacagatattttcttttatgttgtttatatag
||| ||||||||||| || ||||| |||||  |||||||||| || || ||||| ||||| |||||||| ||     | ||||||||||| | | ||  || |    | ||   ||   || |   | |   ||||  || |                                  
CCTCTTCTTCAAGCAAGAGATGGAATTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCTgtaagttcca-agttctctcttttctcgctctttcgctgatggttatc--gattttctag----------------------------------
















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|209719919|gb|BW666002.1|BW666002
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192309196|gb|FG999437.1|FG999437
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|209713657|gb|BW679369.1|BW679369
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|21600628|gb|BQ610959.1|BQ610959
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192326131|gb|FK016958.1|FK016958
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|298198680|gb|HO042043.1|HO042043
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGCAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|151402581|gb|EV272394.1|EV272394
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|298181019|gb|HO022458.1|HO022458
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192299066|gb|FG990394.1|FG990394
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|151411975|gb|EV281786.1|EV281786
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|213608988|gb|DB962914.1|DB962914
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192315185|gb|FK010009.1|FK010009
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|37996453|gb|CF808042.1|CF808042
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192325013|gb|FK015434.1|FK015434
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|209712282|gb|BW668476.1|BW668476
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|15813605|gb|BI785880.1|BI785880
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|213597753|gb|DB960310.1|DB960310
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|209715505|gb|BW682171.1|BW682171
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|58014594|gb|CX701336.1|CX701336
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTNGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|58018793|gb|CX705535.1|CX705535
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192309197|gb|FG999438.1|FG999438
EST:     TAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|192315186|gb|FK010010.1|FK010010
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|8827780|gb|BE211510.1|BE211510
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|213614589|gb|DB969138.1|DB969138
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT
EST: gi|298183805|gb|HO029018.1|HO029018
EST:     TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTGGTTGCT                         ACTGGTGGATATAGTGAGGACATGATTCCAACT
genomic: TAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaa ... gtttatatagACTGGTGGATATAGTGAGGACATGATTCCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCTgtaagttcaataattggctttcacttagcaacttaattgtttaattttgggattgactcgctgacagatattttcttttatgttgtttatatag

- - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA