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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttgcaacaagagccatttctctatttgtatgattagatttgtttcctttctttttctttttttatttcttcctaaattctcttgtttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTTATAAACCCAAATGCCCAGGATCCATTTGTAGTGGGGGTGAGACTGTGGC

Basic information

species Glycine max
transcript GLYMA10G27890.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 8
ttattttgcaacaagagccatttctctatttgtatgattagatttgtttcctttctttttctttttttatttcttcctaaattctc----ttgtttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTTATAAACCCAAATGCCCAGGATCCATTTGTAGTGGGGGTGAGACTGTGGC
   | | |  ||| | |     |   | ||  |   |   |  |  | ||| |  |||||  |||||   || |  ||||   |||    |  |||||  |||||| || ||||||||||||||| |||| ||  ||||||||||||| || || || || || |||||  |||||||| ||||  |||| |||||| | ||||
---tgtggtgacagg-gttgggtggattttcatgcaagctgtatattctccgtggttttttgtttttggattgtatctaatacctcaatttcttttaaccgcagACAGAGAGTGAACTTGTGGAAGCAGTAGACAGAGATTTGAGGAAGATGCTCATTAATCCTAATGCAAAGGATCCACTTGTTTTGGGTGTGAGAGTATGGC
















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|192321103|gb|FK012443.1|FK012443
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|5126795|gb|AI748531.1|AI748531
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACT-GTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|6094914|gb|AW119581.1|AW119581
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACT-GTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|14205990|gb|BG839668.1|BG839668
EST:     GAATTACATTGGAGGAGCAACTAATACTGGGNATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: GAATTACATTGGAGGAGCAACTAATACT-GGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|51342543|gb|CO983523.1|CO983523
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|8284127|gb|BE021686.1|BE021686
EST:     TACTCTNGAATTACATTGGAGGAGCAACTAATACTGGAATTNTATCAAAG                         ACGGACAGTGAACTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTT
EST: gi|58023180|gb|CX709921.1|CX709921
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|192298183|gb|FG991688.1|FG991688
EST:     TACTCTTGAATTACATTGGAGGAACAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|15202240|gb|BI425297.1|BI425297
EST:     CTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: CTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|151394363|gb|EV264234.1|EV264234
EST:     ATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: ATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|19054076|gb|BM732743.1|BM732743
EST:     CTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: CTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
EST: gi|6483224|gb|AW202400.1|AW202400
EST:     TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAG                         ACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT
genomic: TACTCTTGAATTACATTGGAGGAGCAACTAATACTGGAATTTTATCGAAGgtgtgatatt ... ttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctttctttttctttttttatttcttcctaaattctcttgtttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTTATAAACCCAAATGCCCAGGATCCATTTGTAGTGGGGGTGAGACTGTGGC
       ttctttttcttttttt  CT-rich tract
          tttttctttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattttgcaacaagagccatttctctatttgtatgattagatttgtttcctttctttttctttttttatttcttcctaaattctcttgtttaatggcagACGGACAGTGAACTTGTGGAAACAGTTGATCGAGATTTGAGGAAAATCCTTATAAACCCAAATGCCCAGGATCCATTTGTAGTGGGGGTGAGACTGTGGC

- - - tgcaaca
- - - - - - - - -ccatttc
- - - - - - - - - - - - - - - tgtatga