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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatccatccccaataaattaaaatgaataaatttttcatatttgttcttaaggatgcccattatgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAAAGTTCATGGCTGGGAG

Basic information

species Glycine max
transcript GLYMA19G36630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------------------------------------gtaagga-tccatccccaataaattaaaatgaataaa---tttttcatatttgttcttaaggatgcccattatgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAAAGTTCATGGCTGGGAG
                                                                                                  | | | | |||||    || | |      |||| |    | |  | |   |   | |||         |     |  ||||||| | |||| | |||| |||||||| ||||||||||| || ||| ||||||||| ||| ||||||
gtgagtactgggttccactatatgcttattataaataactttgacatagaacattcaacgttgcattaacaactgcagcacattattcttctaaacccatgcacttcatccatgttagaatttttccaatacagtgctatgtaaaacaggattaaagttcttttgatcaccaaactagGTATGCTGACTATATTTTTGGAAATGAAACTGAAGCAAGGACCTTTGCTAAAGTTCGTGGTTGGGAG
















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|10254148|gb|BE821914.1|BE821914
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|192295218|gb|FG986937.1|FG986937
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAT
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|151393153|gb|EV263028.1|EV263028
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|26045675|gb|CA783183.1|CA783183
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTGA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|192304065|gb|FG993895.1|FG993895
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|6455199|gb|AW185882.1|AW185882
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|26045783|gb|CA783264.1|CA783264
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|37996713|gb|CF808302.1|CF808302
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
EST: gi|192329140|gb|FK021127.1|FK021127
EST:     GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC                         GTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA
genomic: GCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatcc ... tgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgaataaatttttcatatttgttcttaaggatgcccattatgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAAAGTTCATGGCTGGGAG
     tgaataaatttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatccatccccaataaattaaaatgaataaatttttcatatttgttcttaaggatgcccattatgtgatttagGTATACGGACTTTGTTTTCGGAAATGAGACTGAAGCAAGAACATTTTCTAAAGTTCATGGCTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC