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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaaattatccatgtctcatagaagtttatcaatgggagactttttaattgatggtcatccattcatttttgtgtatcttgtcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGATTCAGGAAAGAGTACGAAATGCGTAAAATGAAACAG

Basic information

species Glycine max
transcript GLYMA03G33680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33680.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------gtaattgaaattatccatgtctcatagaagtttatcaatg---ggagactttttaattgatggtcatccattcatttttgtgtatcttgtcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGATTCAGGAAAGAGTACGAAATGCGTAAAATGAAACAG
| | | || || |||| | ||| | |||| ||| ||| |||| ||| | | |||| || | ||| || | ||| |||||| ||| || |||||||||||||||||||||||| || ||| |||||| ||||||| |||||||| |||||||| ||
gtgactgttcatgtagagattgtatctatgtattggattttgagtcttatggtaatgtggtttcatt-atttttctaaatgagtggaatgctttcaattaatgcttg-cagttcacttatatgtttcacatgaatgatagATGGACGATTTGACAGTGAATACTTCCAACAAACTGAAGAGTCTAGTCAGTTCAGGCAAGAGTATGAAATGCGGAAAATGAACCAA
















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|9987448|gb|BE661556.1|BE661556
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTNCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|7588839|gb|AW704626.1|AW704626
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|19053265|gb|BM731932.1|BM731932
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|151393190|gb|EV263065.1|EV263065
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|18039839|gb|BM308133.1|BM308133
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAA
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAA
EST: gi|151404741|gb|EV274555.1|EV274555
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|192294446|gb|FG987375.1|FG987375
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|7589461|gb|AW705234.1|AW705234
EST:     TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAG                         ATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: TGGAAGTTGGGCAGCTTCAGCCTCACGTCCTGGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
EST: gi|208030044|gb|GD831526.1|GD831526
EST:     GGAATTAAATTTGATTCAG                         ATGGGAAATTCGACGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT
genomic: GGAATTAAATTTGATTCAGgtaattgaaa ... tcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagactttttaattgatggtcatccattcatttttgtgtatcttgtcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGATTCAGGAAAGAGTACGAAATGCGTAAAATGAAACAG
                                        tcttgtc  CT-rich tract
 tttttaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaaattatccatgtctcatagaagtttatcaatgggagactttttaattgatggtcatccattcatttttgtgtatcttgtcaattccagATGGGAAATTCGATGATGAATACTTCCAACAAACTGAAGAATCAAGTGGATTCAGGAAAGAGTACGAAATGCGTAAAATGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA