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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAAGATAGTTAGTGTGAGGATCAGAAGGAATTTTGCTTTTGTTCAATATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaatgtatttggatatttgtttcaaacagttaagcatttctgtttcatgtttctttcaaatctgtcattggccactagtcattgtatgaccaat...

Basic information

species Glycine max
transcript GLYMA20G29460.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G29460.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0100g00450.t01 (Vitis vinifera), 5'ss of exon 4
ATGGAAAGATAGTTAGTGTGAGGATCAGAAGGAATTTTGCTTTTGTTCAATATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaa-------tgtatttggatatttgtttcaaaca-gttaagcatttctgtttcat-gtttctttca-----aatctgtcattggccactagtcattgtatgaccaat----------------------------------------------------------------
|||| || ||| | |   | |||||||||||||||||||| ||| |||| ||||||||| | || ||||| |  |||||| |||| |||||||| |||||||   ||         | | ||||  | ||| ||    ||| | |    | || |||  |||  | | || ||     ||  | |   ||     |  | | ||| | |    |                                                                
ATGGGAAAATATTAAACATAAGGATCAGAAGGAATTTTGCATTTATTCAGTATGAATCACAAGAGGATGCCACTAGAGCATTGGAGGCTACAAACATGAGgtcgattctcctcatttttctttgactttttattctgtacatgattgttagttttgtagcattatatattgcatgaaaaaaatcttgctgctacatgtttactgtttaagggctcattttattatgaatgtttagtagcttttttatgatgatttttctgtttattctggatgtacag
















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|254329145|gb|GR833517.1|GR833517
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
EST: gi|6454368|gb|AW185051.1|AW185051
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTTGAAGCTACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGGTGAAATTGCTTGT-AAAGATGATG
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCT-GTTAAAGATGATG
EST: gi|208171682|gb|GD967165.1|GD967165
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
EST: gi|209705492|gb|BW668070.1|BW668070
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACNAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
EST: gi|298175607|gb|HO015126.1|HO015126
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAG                         CAAGTTACTGGAT
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGAT
EST: gi|9986286|gb|BE660394.1|BE660394
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGGTGAATTTGCTGGTAAAGATGATGA
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
EST: gi|7796093|gb|AW781490.1|AW781490
EST:     TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
genomic: TATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
EST: gi|207794815|gb|GD764902.1|GD764902
EST:     GCACTGGAAGCCACAAATATGAG                         CAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA
genomic: GCACTGGAAGCTACAAATATGAGgtgagttaat ... cttccaacagCAAGTTACTGGATCGAGTTATTTCTGTTGAATTTGCTGTTAAAGATGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAAAGATAGTTAGTGTGAGGATCAGAAGGAATTTTGCTTTTGTTCAATATGAATCAGAGGATGATGCTAGCAGAGCACTGGAAGCTACAAATATGAGgtgagttaatgtatttggatatttgtttcaaacagttaagcatttctgtttcatgtttctttcaaatctgtcattggccactagtcattgtatgaccaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG