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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaacaatatagcctctcaaatcatattttcagtatttggtgaagttgttagctgcttattattgcattaattactgagttatctttttttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCTATTG

Basic information

species Glycine max
transcript GLYMA16G19560.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 23
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 22
taaaaacaatatagcctctcaaatcatattttcagtatttggtgaagttgttagctgcttattattgcatta-attactgagttatctttttttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCTATTG
           |||       |||| |  |||   |||    | |   | ||   || || || |||  | | || |  |||| ||      | ||| |||| ||| || ||| | ||||  ||  | |   | || | ||| |||||    || || ||||||||||||||||||||||||||||| || |  ||||  |
----------gtaggactaataatcgttatttttatatc-aatcagccttttccgtgtttgttgttggctgatataatagagtgat------tgcatacagAGTCCTCCACCACTGGATGCACCGTTGAGCATAATCGAAAAAGATCCGAATGCCAAAGATATAAAGTGGGAAGATGATGGAGTGCTTGTGAATTCTACGG

upper sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 23
lower sequence: AT5G58140.3 (Arabidopsis thaliana), 3'ss of exon 21
taaaaacaatatagcctctcaaatcatattttcagtatttggtgaagttgttagctgcttattattgcatta-attactgagttatctttttttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCTATTG
      ||   |||       |||| |  |||   |||    | |   | ||   || || || |||  | | || |  |||| ||      | ||| |||| ||| || ||| | ||||  ||  | |   | || | ||| |||||    || || ||||||||||||||||||||||||||||| || |  ||||  |
-----gcatggtaggactaataatcgttatttttatatc-aatcagccttttccgtgtttgttgttggctgatataatagagtgat------tgcatacagAGTCCTCCACCACTGGATGCACCGTTGAGCATAATCGAAAAAGATCCGAATGCCAAAGATATAAAGTGGGAAGATGATGGAGTGCTTGTGAATTCTACGG
















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|151399535|gb|EV269406.1|EV269406
EST:     AGCAACATCCTTTTT-CCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
EST: gi|27809437|gb|CB063859.1|CB063859
EST:     AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
EST: gi|208157486|gb|GD955976.1|GD955976
EST:     AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
EST: gi|6481668|gb|AW200939.1|AW200939
EST:     AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
EST: gi|12690506|gb|BG156842.1|BG156842
EST:     AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
EST: gi|193729552|gb|FK666066.1|FK666066
EST:     AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATG                         ACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG
genomic: AGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattct ... tttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgttagctgcttattattgcattaattactgagttatctttttttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCTATTG
                      cattaat  putative branch site (score: 3)
                                    ttatctttttttcat  putative PPT
             ttattattgcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaacaatatagcctctcaaatcatattttcagtatttggtgaagttgttagctgcttattattgcattaattactgagttatctttttttcatgcagACTCCACCCCCATTAGATGTTCCTCTTAAATTGATAGGAAACGATCCCGTGGCAAAGGATATAAAGTGGGAAGATGATGGAGTGCTAGTTAGCTCTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- aaaacaa
- - - - - - - cctctca
- - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - -tagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgag