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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgcttaggatgcttgtgtctaattagttaaacaaatgttcattgctaatgcaaaagctggagctctttagacactcatctctttgtgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGAGACAATTTCTACGATGATGGATTGACTGGTATAGATGACCCTGCATTTG

Basic information

species Glycine max
transcript GLYMA05G33640.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G33640.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 3'ss of exon 1
---ttttttgcttaggatgcttgtgtctaattagttaaacaaatgttcattgctaa-tgcaaaagctggagctctttagacactcatctctttgtgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGAGACAATTTCTACGATGATGGATTGACTGGTATAGATGACCCTGCATTTG
   || | |  |||   ||  |   | |  | |     | |  | ||  ||  ||| |   ||||    |     |||   |   | |  ||| |  ||| |||||||| | |||||  |  ||| ||||||| ||||| || |||||||| || |||||||||||||| |||||| | |||||  | |||||||  || ||||
tatttgtattattaaagtgaatactttttttaaaactga-aggtattattttttaaatagcaaagacaaacaatattaagtatgga-caatttat-catg-cagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGTGACAATTTCTACGAGGATGGACTCACTGGCGTCGATGACCAGGCGTTTG
















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|209707341|gb|BW670620.1|BW670620
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|151396212|gb|EV266089.1|EV266089
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|18848901|gb|BM568011.1|BM568011
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|208334648|gb|GE126671.1|GE126671
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193396109|gb|FK361864.1|FK361864
EST:     ACCAATCTCAAGTTGCCACTCTAGT                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTG
genomic: ACCAATCTCAAGTTGCCACTC-AG-gtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTG
EST: gi|193396109|gb|FK361864.1|FK361864
EST:     ACCAATCTCAAGTTGCCACTCTAGT                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTG
genomic: ACCAATCTCAAGTTGCCACTC-AG-gtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTG
EST: gi|151406975|gb|EV276790.1|EV276790
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193724982|gb|FK659694.1|FK659694
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|120534060|gb|EH262193.1|EH262193
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|207712526|gb|GD694326.1|GD694326
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|298163376|gb|HO012109.1|HO012109
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|10237583|gb|BE806471.1|BE806471
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|298197299|gb|HO044778.1|HO044778
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193668311|gb|FK608531.1|FK608531
EST:     GAGACTGGGGAGGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193528436|gb|FK485184.1|FK485184
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|254314578|gb|GR829571.1|GR829571
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|298189993|gb|HO032114.1|HO032114
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|298178541|gb|HO024276.1|HO024276
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193434090|gb|FK400186.1|FK400186
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTT
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTT
EST: gi|298171038|gb|HO016070.1|HO016070
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCACTCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|9987619|gb|BE661727.1|BE661727
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|192299309|gb|FG990734.1|FG990734
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|193558421|gb|FK515282.1|FK515282
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAGTATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|298170795|gb|HO015771.1|HO015771
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|192328997|gb|FK019696.1|FK019696
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|208077317|gb|GD877858.1|GD877858
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|192301322|gb|FG990212.1|FG990212
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
EST: gi|308098252|gb|HO759993.1|HO759993
EST:     GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAG                         ATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA
genomic: GAGACTGGGGAAGGAAAGGAACATACAACCAATCTCAAGTTGCCACTCAGgtcttcatcc ... tgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctaatgcaaaagctggagctctttagacactcatctctttgtgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGAGACAATTTCTACGATGATGGATTGACTGGTATAGATGACCCTGCATTTG
  tgctaat  putative branch site (score: 2)
                                     tctctttgt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgcttaggatgcttgtgtctaattagttaaacaaatgttcattgctaatgcaaaagctggagctctttagacactcatctctttgtgtatgtcagATGGGAAGGGTTGCTGCAAAGTTAAATATCGACTTTGTGATATCCACTGGAGACAATTTCTACGATGATGGATTGACTGGTATAGATGACCCTGCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA