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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattatttacctattgctgccaatcattgattttttcacacacttaggtcagtccattaaatttcaaaatgaaaattttcatgtatttttgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG

Basic information

species Glycine max
transcript GLYMA19G35370.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 9
-----gtaaggattatttacctattgctgccaatcattgattttttcacacacttaggtcagtccattaaatttcaaaatgaaaattttcatg--tatttttgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG
      |   ||    || || |||  |      |||| |  | ||        ||  ||| || ||  |||    |  |      |   |||  |||| |  ||| |||| |||||| | || |||| ||| ||||| |||||||| ||||||||| ||||||||||||||
gtatgcttcagaccccttgccaatttttcttttgcattcaagtcttt-----tataattcattctatgcaatgctcattttgtccatccaatgcttattctacttgtacagTTTTGGTACAGTACTTGTTTCCCGAGCGATTAGAGCTGCTCATTGTTTGACTTCAATTCAG
















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|193667497|gb|FK611009.1|FK611009
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTG
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTG
EST: gi|26058982|gb|CA801896.1|CA801896
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGGTCGGTGCTTGCTTCACGAGCAATTAGAGCA
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCA
EST: gi|10847791|gb|BF071604.1|BF071604
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
EST: gi|21889859|gb|BQ743072.1|BQ743072
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
EST: gi|208119661|gb|GD915200.1|GD915200
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTGCTTGCTTCAC
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCAC
EST: gi|193686900|gb|FK632523.1|FK632523
EST:     TATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
genomic: TATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
EST: gi|12690329|gb|BG156665.1|BG156665
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATCTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
EST: gi|26047106|gb|CA783997.1|CA783997
EST:     GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAAC                         ATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC
genomic: GCACACCAAGTAATGTATGAGCTGCGCATATATTCCCTCGAGGAGGCAACgtaaggatta ... tgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggtcagtccattaaatttcaaaatgaaaattttcatgtatttttgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG
                                         tttttgtt  CT-rich tract
           attaaatttcaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattatttacctattgctgccaatcattgattttttcacacacttaggtcagtccattaaatttcaaaatgaaaattttcatgtatttttgttgaacagATTTGGTTCGGTGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA