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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtctcttttgtataaagttagttcttcattatatatttatataccatgaaggtaactgactagttaaaaacttaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTCCGTGACACAAGACTTGAGGTCGTGATCAACGATGCCAG

Basic information

species Glycine max
transcript GLYMA20G28340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g03200.t01 (Vitis vinifera), 3'ss of exon 4
gtatagtctcttttgtataaagttagttcttcattatatatttatatacc--atgaaggt-aactgactagttaaaaact-taaaatccatgtgcttgc-tcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTCCGTGACACAAGACTTGAGGTCGTGATCAACGATGCCAG
           |  ||  ||||  |    |     | | |   ||   |   |  || || ||   || ||||  | | |  | | |  || |  || | | ||||||||||||||| ||||||||||||| ||||| ||||| ||||  ||||| ||| ||||  | ||||||||| | || ||||||||||||||
--------aaatgagtggaaagagaaagttgggggagaaaccaatcctcttgacaaatgtcaaaatacaagttttatattacatacttaatattgttccatggagcagGAGGTGGTGGATTTCTGCAAATCATACTTGGTGGTAAACAGAGAAGCTTTCTGTGATCCCAGACTTGAGCTTGTCATCAACGATGCCAG
















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|9565859|gb|BE475368.1|BE475368
EST:     TGCTTATGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCTAATC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATC
EST: gi|298184543|gb|HO029756.1|HO029756
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTAC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTAC
EST: gi|298178935|gb|HO024670.1|HO024670
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATGGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
EST: gi|298187240|gb|HO034389.1|HO034389
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
EST: gi|15203776|gb|BI426544.1|BI426544
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAAGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
EST: gi|8283967|gb|BE021526.1|BE021526
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
EST: gi|18040061|gb|BM308355.1|BM308355
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC
EST: gi|192327192|gb|FK017729.1|FK017729
EST:     TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAG                         GAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAG-AAGCATTC
genomic: TGCTTAGGCATAAGACTATAGACAAAGTTGTAATGTGTGACATAGATGAGgtatagtctc ... gctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgaaggtaactgactagttaaaaacttaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTCCGTGACACAAGACTTGAGGTCGTGATCAACGATGCCAG
          aactgac  putative branch site (score: 2)
                                          cttgctc  putative PPT
                 tagttaaaaacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtctcttttgtataaagttagttcttcattatatatttatataccatgaaggtaactgactagttaaaaacttaaaatccatgtgcttgctcgagcagGAGGTGGTGAATTTCTGCAAATCGTACTTTGTGGTGAACAAGGAAGCATTCCGTGACACAAGACTTGAGGTCGTGATCAACGATGCCAG

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