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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataagctaattcaaatttaaacatgtgtaactttaaattcccgtaaaagtatttctaacattactgtttttttttttttttttttttttttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGGGTGTTTGGAAGCTATGACTATAATCCATTGCTTGAGTCCTTGGAAGGAA

Basic information

species Glycine max
transcript GLYMA08G45210.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 13
aataagctaattcaaatttaaac---atgtgtaactttaaattcccgtaaaagtatttctaacattactgtttttttttttttttttttttttttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGGGTGTTTGGAAGCTATGACTATAATCCATTGCTTGAGTCCTTGGAAGGAA
  |||| ||  |  |  | ||      |||  ||||||  ||||   | | | |  || |||    |     | || ||   || ||| ||    | | | |||||||||| || || || |||||||| || ||| ||||||| |||||||| |  ||||| |||||||||||| | ||  |  | || ||| | ||||| |
-gtaagatagcttcagctaaacttcactgttgaacttttcattcaactcatatttcttataagtagatgagctattattgacttgtttcttacaatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGCGCTTTTGGCAGCTATGACTATGAACCTCTCTTGGATTCCCTTGAAGGGA

upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------------------aataagctaattcaaatttaaacatgtgtaactttaaattcccgtaaaagtatttctaacattactgtttttttttttttttt-----ttttttttttttta---------tagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGGGTGTTTGGAAGCTATGACTATAATCCATTGCTTGAGTCCTTGGAAGGAA
                                              |    |||||   | |     || | | |||  ||    || | ||  |  |   | |||   ||| | |    |      ||||| |   | ||         |||||||||||||||||||| || |||||||||||| ||||| | |  ||||| |||||||| ||||| || |||  |||| | ||||| ||  | || || |
gtatgtcactctctccttttctcccttacataaatttttgtctctgtggaacaaatgcgagccaccataccatgaaaggccttataatgaatcacctatgcttctggactttatctgacatgaaacgtttttgtgcctgtaaaaactgattagTTCAAACCCGATCCTCGGTTCGAAGAGGCAAAGCAGTTTGTCAAAAGTGGAGTGTTTGGGAGCTACGATTATGGTCCACTCCTTGATTCTCTTGAGGGTA
















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|17963826|gb|BM270570.1|BM270570
EST:     CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
genomic: CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
EST: gi|10231261|gb|BE800149.1|BE800149
EST:     CTCGACTGAGGAAGGAAAGAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
genomic: CTCGACTGAGGAAGGAAAGAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
EST: gi|15286007|gb|BI469889.1|BI469889
EST:     CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
genomic: CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
EST: gi|193470273|gb|FK435066.1|FK435066
EST:     GGAAGGAAAGAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
genomic: GGAAGGAAAGAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
EST: gi|9902492|gb|BE611460.1|BE611460
EST:     GAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
genomic: GAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGG
EST: gi|26047983|gb|CA784613.1|CA784613
EST:     CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTG                         TTCAAACCCGATCCTCGATTTGAAGAGGCAAAG
genomic: CCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTGgtatgcagta ... ttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtatttctaacattactgtttttttttttttttttttttttttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGGGTGTTTGGAAGCTATGACTATAATCCATTGCTTGAGTCCTTGGAAGGAA
        ttctaac  putative branch site (score: 1)
              cattactgtttttttt  CT-rich tract
               attactgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataagctaattcaaatttaaacatgtgtaactttaaattcccgtaaaagtatttctaacattactgtttttttttttttttttttttttttttttatagTTCAAACCCGATCCTCGATTTGAAGAGGCAAAGAAGTTTATTAGGAGTGGGGTGTTTGGAAGCTATGACTATAATCCATTGCTTGAGTCCTTGGAAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - -acatgtg