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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtagcctgtcactctatttttcagagatatataaatcaatgatgcaatttcttgttctgataattgcaatccggttgggttctgataatgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTATTGATGAAGTTGCCAGCATGTAATTTGAAGTTGAAGCACTAGCATATTTG

Basic information

species Glycine max
transcript GLYMA17G11790.3
intron # 9
splice site 3'
intron type U2

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|209701995|gb|BW670532.1|BW670532
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAG---TGCT-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193538845|gb|FK496373.1|FK496373
EST:     AAGTACCGACTGACTCTTTTGTTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: AAGTACCGACTGACTCTTTTG-TACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|192320104|gb|FK014174.1|FK014174
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAGAACTGGAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208306843|gb|GE110074.1|GE110074
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|254335242|gb|GR846739.1|GR846739
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193635119|gb|FK579812.1|FK579812
EST:     AAGTACCGACTGACTCTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: AAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|151411194|gb|EV281005.1|EV281005
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAA
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAA
EST: gi|254324087|gb|GR840512.1|GR840512
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193681333|gb|FK624469.1|FK624469
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209706577|gb|BW667830.1|BW667830
EST:     CTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: CTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209728181|gb|BW651616.1|BW651616
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209714893|gb|BW682058.1|BW682058
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|192320103|gb|FK014173.1|FK014173
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAGAACTGGAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|17153281|gb|BM143214.1|BM143214
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAA
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAA
EST: gi|193392304|gb|FK360129.1|FK360129
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATT
EST: gi|58025077|gb|CX711818.1|CX711818
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|31459027|gb|CD401055.1|CD401055
EST:     CAAGAAAGTACCGACTGACTCTTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: CAAGAAAGTACCGACTGACTC-TTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193332504|gb|FK301622.1|FK301622
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208091965|gb|GD890556.1|GD890556
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193663472|gb|FK602762.1|FK602762
EST:     AATCAGTACTGGCAG                         GGGACACAATCGCAGAAGAAGAAAAACTGAAGCATTTTCTATTGAAAGTTA
genomic: AATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAG-AAAACTGAAGCATTTTCTATTGAAAGTTA
EST: gi|151399107|gb|EV268978.1|EV268978
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGCAG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208316365|gb|GE114049.1|GE114049
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|9899557|gb|BE608525.1|BE608525
EST:     GCAAGANAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209705503|gb|BW673524.1|BW673524
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|7685096|gb|AW755744.1|AW755744
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|13789618|gb|BG652209.1|BG652209
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|254344612|gb|GR855483.1|GR855483
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGG--G                         G--ACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|13311818|gb|BG405469.1|BG405469
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTAC---T-G                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGTAGgttccctcca ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaatttcttgttctgataattgcaatccggttgggttctgataatgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTATTGATGAAGTTGCCAGCATGTAATTTGAAGTTGAAGCACTAGCATATTTG
                                     ttctgat  putative branch site (score: 3)
               tgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtagcctgtcactctatttttcagagatatataaatcaatgatgcaatttcttgttctgataattgcaatccggttgggttctgataatgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTATTGATGAAGTTGCCAGCATGTAATTTGAAGTTGAAGCACTAGCATATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC