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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattatgtagattttaatgcattgatttgaatgatacgatgcaaggctcttaaacatgattatttttaacccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG

Basic information

species Glycine max
transcript GLYMA03G39530.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39530.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------gtaatattatgtagattttaatgcattg-atttgaatgatacgatgcaaggctcttaaacatgattatttttaacccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG
                                                                   |  |  | | |   || |  | || || || ||   ||    ||  |   ||     |    | |  ||||   |   |||||||| || |||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||| ||||  | ||||||
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|192308192|gb|FK001290.1|FK001290
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         -TCGGTGCCCATTATTTTGAGGAAG-AAATGTGCAGTTAGATGCAA
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAA
EST: gi|192303326|gb|FG995620.1|FG995620
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|37997277|gb|CF808866.1|CF808866
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|151403727|gb|EV273537.1|EV273537
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|7692294|gb|AW760404.1|AW760404
EST:     TTGAGTTCATAGATGAACAACAAACAGTGGAAGTAAATGGTAAAATGCAC                         GTCGGAGCCCATTATTTTGAGGAATGAAATGTGCAGGTAGATGCGAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|192303311|gb|FG995619.1|FG995619
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAA-TGCAG                         GTCGGTGCCCATTATTTTGAGGAAG-AAATGTGCAGTTAGATGCAAA-CAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|37996140|gb|CF807729.1|CF807729
EST:     GTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: GTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|298184842|gb|HO030055.1|HO030055
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|9987385|gb|BE661493.1|BE661493
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|151397822|gb|EV267695.1|EV267695
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGG
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGG
EST: gi|58019780|gb|CX706522.1|CX706522
EST:     TTGAGTTCAAAGATGACCAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|10231910|gb|BE800798.1|BE800798
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAG                         GTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCGAAACAT
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACAT
EST: gi|151399910|gb|EV269781.1|EV269781
EST:     TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGG-TAAA-TGCAG                         -TCGGTGCCCATTATTTTGA
genomic: TTGAGTTCAAAGATGAACAACAAACAGTGGAAGTAAAGGGTAAAATGCAGgtaatattat ... ccattttcagGTCGGTGCCCATTATTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatgatacgatgcaaggctcttaaacatgattatttttaacccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG
                                      ttttaac  putative branch site (score: 2)
                                            cccattttc  CT-rich tract
                      tcttaaacatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattatgtagattttaatgcattgatttgaatgatacgatgcaaggctcttaaacatgattatttttaacccattttcagGTCGGTGCCCATTATTTTGAGGAAGGAAATGTGCAGTTAGATGCAAAACATGAATGCAAAGATGCAACTCTTTTTCAG

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