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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagctgctaagcaagttatattttgcatgatatatctgaatatcaaacctaacagtaattaaatcttttgcgttaattgcatcattcttttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAATTTGTGATGTA

Basic information

species Glycine max
transcript GLYMA16G09890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g01400.t01 (Vitis vinifera), 3'ss of exon 4
gaagctgc-taagcaagttat-attttgcatgatatatctgaatatcaaacctaacagtaat-taaatcttttgcgttaattgcatcattcttttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAATTTGTGATGTA
 ||  | | |    |||||   | || |||  |  |||   |   | | |  | |    | |    || || |   ||| |    ||  ||| |  | ||||| | | ||| || || || |||||||||||||| ||||||||||| |||||| |||| ||||| ||||||||||||||    | ||   || | |      
-aacttacatttataagttgccaattagcaaaacctattaaagattgatatttgattagagtgcttattttatatcttactgaagtc--tctatgtcatgcagACGAAAGGCCGGGCCCATGATGATGAAGCAATTGAGAAAATGTTGAATGACTTGTCTTTGATCAAGAAATTTGAATAGTAGCCTCTTCATATTTAGAACC
















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|192329760|gb|FK022984.1|FK022984
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|14196190|gb|BE657977.2|BE657977
EST:     AGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: AGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|208326961|gb|GE123709.1|GE123709
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|207762346|gb|GD732059.1|GD732059
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|208191571|gb|GD991015.1|GD991015
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|7145703|gb|AW507625.1|AW507625
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|208277131|gb|GE080802.1|GE080802
EST:     TTTGCCCAGAAACTGTGGAGGAAGCCATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|10254879|gb|BE822645.1|BE822645
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|208244951|gb|GE042086.1|GE042086
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|192303824|gb|FG998176.1|FG998176
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|7285750|gb|AW598237.1|AW598237
EST:     GCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: GCTATTGCTATGGTTCCATCTATCAAGgtaaaaatag ... ttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacctaacagtaattaaatcttttgcgttaattgcatcattcttttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAATTTGTGATGTA
                                     tcattcttttacct  CT-rich tract
         agtaattaaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagctgctaagcaagttatattttgcatgatatatctgaatatcaaacctaacagtaattaaatcttttgcgttaattgcatcattcttttacctgcagTCAAGAGGACGAGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAATTTGTGATGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-aagctgc
- - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - -tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcatc