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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtgtgtgtgatttggaaatttttgaacataaagtgtatttcatttcttggtgtttttgttcaacgtttactttgccatgcataaatctgtgctgatattctttgttctttttttgctgttgaattttgtgttgtctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA

Basic information

species Glycine max
transcript GLYMA18G46390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 2
ggtgtgtgtgatttggaaatttttgaacataaagtgtatttcatttcttggtgtttttgttcaacgtttactttgccatgcataaatctgtgctgatattctttgttctttttttgctgttgaattttgtgttgtctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA-
                   |  ||||   | ||   || ||    ||||| |   | ||       |||  |||   |||  ||| ||   |  ||  |    ||||  || |     ||||    | |  || | |   | |||||| | || ||||| |||||||| || ||||||||| | |||||||||||||| ||||| ||  || 
------------------gtacttgat--tgaatactactttgcctcttgttcaatctggct---ctttgattt---atg-gtaattccaag--gaattaaaatgtttcttgtgcttagttggtaatagcttttttttattccagGTTATTACAGTTGGGGTTGTTGGAGGATCTGACCTTGTTAAGATATCAGAGCAGCTTGGAAGTTCAG
















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|213618074|gb|DB963707.1|DB963707
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACGGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|192303883|gb|FG998235.1|FG998235
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|213617059|gb|DB961539.1|DB961539
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACGGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|16348803|gb|BI974398.1|BI974398
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|192298879|gb|FG987624.1|FG987624
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|193590717|gb|FK544590.1|FK544590
EST:     AGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: AGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|298189249|gb|HO037652.1|HO037652
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACGGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|209717163|gb|BW657626.1|BW657626
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACGGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|197664690|gb|FD480363.1|FD480363
EST:     AGGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACGGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: AGGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|193455949|gb|FK417042.1|FK417042
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|192306982|gb|FG999987.1|FG999987
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|6727118|gb|AW311472.1|AW311472
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|192299912|gb|FG991786.1|FG991786
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
EST: gi|151402943|gb|EV272756.1|EV272756
EST:     GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAA                         GGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA
genomic: GGTGGTCACACCGGAGATGTTGACATTCATGCAAGAACTGCGGAAggtgtgtgtg ... tctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgatattctttgttctttttttgctgttgaattttgtgttgtctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA
 tgctgat  putative branch site (score: 3)
            tttgttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtgtgtgatttggaaatttttgaacataaagtgtatttcatttcttggtgtttttgttcaacgtttactttgccatgcataaatctgtgctgatattctttgttctttttttgctgttgaattttgtgttgtctgggtacaGGTTGTAACTGTTGGAGTTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA