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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatctcctttgtataaagttaactcttcattgtctatttatataccatggagctcattgacgagttaaaaacttaaaaattaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTCCGTGATCAGAGACTTGAGGTCGTGATCAACGACGCCAG

Basic information

species Glycine max
transcript GLYMA10G39440.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G39440.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g03200.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaatctcctttgtataaagttaactcttcattgtctatttatataccatggagctcattgacgagttaaaaacttaaaaattaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTCCGTGATCAGAGACTTGAGGTCGTGATCAACGACGCCAG
  |||           | ||||||        |    | ||     |  ||    |   |   || ||||  | | |  | | |||| ||     || |   | ||||||||||||||| ||||||||||||| ||||| || || ||||  ||||| ||| ||||||  ||||||||| | || |||||||| |||||
--aaatgagtggaaagagaaagttgggggagaa--accaatcctcttgaca-aatgtcaaaatacaagttttatattacatacttaatat-----tgttccatggagcagGAGGTGGTGGATTTCTGCAAATCATACTTGGTGGTAAACAGAGAAGCTTTCTGTGATCCCAGACTTGAGCTTGTCATCAACGATGCCAG
















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|192331927|gb|FK026711.1|FK026711
EST:     TGCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
genomic: TGCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAGgtaaaatctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
EST: gi|192295039|gb|FG986758.1|FG986758
EST:     GCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
genomic: GCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAGgtaaaatctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
EST: gi|151411311|gb|EV281122.1|EV281122
EST:     TGCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
genomic: TGCTCAGGCATAAGACTATAAACAAAGTTGTAATGTGTGACATAGATGAGgtaaaatctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
EST: gi|298183097|gb|HO028360.1|HO028360
EST:     TAAACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC
genomic: TAAACAAAGTTGTAATGTGTGACATAGATGAGgtaaaatctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcattgacgagttaaaaacttaaaaattaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTCCGTGATCAGAGACTTGAGGTCGTGATCAACGACGCCAG
   cattgac  putative branch site (score: 3)
                                          cttgctc  putative PPT
           agttaaaaacttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatctcctttgtataaagttaactcttcattgtctatttatataccatggagctcattgacgagttaaaaacttaaaaattaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTAGTTGTGAACAAGGAAGCATTCCGTGATCAGAGACTTGAGGTCGTGATCAACGACGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA