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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcaattttcactttttattcttcctcatgctattatgtgcaaggagattttgttcctggtgatgggaagtaaagtgatttatacctgcattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA

Basic information

species Glycine max
transcript GLYMA18G47190.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
ttttcaattttcactttttattcttcctcatgctattatgtgcaaggagattttgttcctggtgatgggaagtaaagtgatttatacctgcatttt-caggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA
                 | |       | |    |  |     |  |  |  |   |    || |        || |   ||| |    | ||||| ||||| |||||  | ||||| ||||| || ||||| | |||||| ||||||||||| || |||||||| |||||||||||  |    ||  | || | |   | 
----------------gtcagagaagataacaacagaacacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG-

upper sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
-ttttcaattttcactttttattcttcctca-tgctattatgtgcaaggagattttgtt---cctggtgatgggaagtaaagtgatttatacctgcattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA
      |||| |||        | ||  | | ||| | ||     |      ||||||    ||  |||         | |  ||||||    ||  ||| ||||| || ||| | || ||||||||||||||||| |||||||| ||||| |||||||| |||||||| ||||||||||||||||| || || || ||||| | 
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagattta---atgt-tttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG-
















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|7691739|gb|AW759861.1|AW759861
EST:     GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGG                         AGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
genomic: GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGGtgacatttat ... cattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
EST: gi|13788835|gb|BG651426.1|BG651426
EST:     GAAGCTTGGATATGCATCTGGACTACGCGGNGGTCTTGTGAAACTACAGG                         AGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
genomic: GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGGtgacatttat ... cattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
EST: gi|192305931|gb|FG993591.1|FG993591
EST:     GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGG                         AGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
genomic: GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGGtgacatttat ... cattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACT
EST: gi|26058879|gb|CA801793.1|CA801793
EST:     GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGG                         AGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCA
genomic: GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGGtgacatttat ... cattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCA
EST: gi|105634970|gb|DW247718.1|DW247718
EST:     GAAGCTTGGGTATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGG                         AGGAGAATCTTTCAGCTATGAATACAGATCCTTGGT
genomic: GAAGCTTGGATATGCATCTGGACTACGCGGTGGTCTTGTGAAACTACAGGtgacatttat ... cattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagattttgttcctggtgatgggaagtaaagtgatttatacctgcattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA
                                             cattttc  CT-rich tract
                           taaagtgatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcaattttcactttttattcttcctcatgctattatgtgcaaggagattttgttcctggtgatgggaagtaaagtgatttatacctgcattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - - tgcaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacctg