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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttatgtagattttttatgcattgatgtgaatgacacgatgcaaggctcttaaacattattttttttaacccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG

Basic information

species Glycine max
transcript GLYMA19G42150.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G42150.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------gtaatgttatgtagattttttatgcattgatgtgaatgacacgatgcaaggctcttaaacattattttttttaacccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG
                                                                   |  || | | |   || ||| |   |  |||||   ||    ||  |   ||     |    | || ||||   |   |||||||| || |||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||| ||||  | ||||||
gtatttttctttaactgattctagtgtatatatgatacaacttttaggacttctttattaagtcccttggtgctttctgttttatttttcagtgcatgtgccagaattaatttagacctacattatgccaattattttgttcttctttcagGTGGGGGCCCATTACTTTGAAGAGGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAGGATTCAACAATATTTCAG
















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|27425324|gb|CA936844.1|CA936844
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|9819909|gb|BE555352.1|BE555352
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|9203355|gb|BE329641.1|BE329641
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|7234639|gb|AW569975.1|AW569975
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|192295752|gb|FG992593.1|FG992593
EST:     TTGAGTTCAAAGATGGAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         -TTGGTGCCCATTATTTTGAGGAAG-AAATGTGCAGTTAGATGCAAA-CAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|151412172|gb|EV281984.1|EV281984
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|14516434|gb|BI095106.1|BI095106
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|14258566|gb|BG881474.1|BG881474
EST:     TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCACTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAAAAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatgttat ... ccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaatgacacgatgcaaggctcttaaacattattttttttaacccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG
                                      ttttaac  putative branch site (score: 2)
                                            cccattttc  CT-rich tract
                        ttaaacattatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttatgtagattttttatgcattgatgtgaatgacacgatgcaaggctcttaaacattattttttttaacccattttcagGTTGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG