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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactacgtgtcagttttttattctttgatgcatacatggctatattaaatttaaacgcacacaattgcctaatgtgtatgcatgtgtttttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAACAAGCATTACTTAGTGAACTGAGCTCTTTCAGT

Basic information

species Glycine max
transcript GLYMA11G33700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g12630.2 (Oryza sativa), 3'ss of exon 3
---ctactacgtgtcagttttttattctttgatgcatacatggctatattaaatttaaacgcacacaattgcctaatgtgtatgcatgtgtttttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAACAAGCATTACTTAGTGAACTGAGCTCTTTCAGT
    |  |   |   |       ||||| || ||  ||  | | ||||  | |||      || || |    |  |    | ||        ||| | |  || |||||||| || ||||| || ||||||||||| || || ||||| ||||| ||||||||||||||||| ||| | |||||||| ||||  || |||  |
acttttttttttaaaaaaaaacaattctatggtgt-tatttag-tatacaacattgttgtccatactagcatcctaaccat-tgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
















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|192296135|gb|FG989495.1|FG989495
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|209722386|gb|BW665859.1|BW665859
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|213609040|gb|DB957428.1|DB957428
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGANAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|7147501|gb|AW509423.1|AW509423
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTGTCTCANGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|151403447|gb|EV273257.1|EV273257
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGCAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|192299879|gb|FG990087.1|FG990087
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAA-GATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|14011917|gb|BG726839.1|BG726839
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|120534693|gb|EH262826.1|EH262826
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|298165886|gb|HO008857.1|HO008857
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|120534677|gb|EH262810.1|EH262810
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|10233723|gb|BE802611.1|BE802611
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|12691145|gb|BG157481.1|BG157481
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|209705734|gb|BW661402.1|BW661402
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|11688459|gb|BF596135.1|BF596135
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGNGTCAAAGATCTTTTCAACATTTATTGGTTNTCTCAAGAGCA
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCA
EST: gi|20813171|gb|BQ297649.1|BQ297649
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
EST: gi|5677088|gb|AI938218.1|AI938218
EST:     GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGC                         GGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC
genomic: GAGAAGTATCCCAGCCCCCCATTGTTGACCCCACCTGAAAAGGCCACGGCgtatgcattt ... ttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatttaaacgcacacaattgcctaatgtgtatgcatgtgtttttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAACAAGCATTACTTAGTGAACTGAGCTCTTTCAGT
                      gcctaat  putative branch site (score: 3)
                                      tgtgtttttttcttt  putative PPT
                                        tgtttttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactacgtgtcagttttttattctttgatgcatacatggctatattaaatttaaacgcacacaattgcctaatgtgtatgcatgtgtttttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAACAAGCATTACTTAGTGAACTGAGCTCTTTCAGT

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