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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaactttatactattaataatattctaattaaattatatatactagttttcaaatttttgcttcaaccttgtttatttgctatgattggaatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGGAACAGAACAGGACAACCTTACATTTTGCAAACAAATGTGTTCACCGGAG

Basic information

species Glycine max
transcript GLYMA16G04960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G06850.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaactttatactattaataatattctaattaaattatatatactagttttcaaatttttgcttcaaccttgtttatttgctatgattggaatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGGAACAGAACAGGACAACCTTACATTTTGCAAACAAATGTGTTCACCGGAG
  || | | |   | || | |    ||||| |   ||  || |  |  ||| ||     || || |||  | ||||||    || | | |  |     || |||| |||   ||    ||||| || |||||||| ||||||||| | || |||||||||||||||||    || || || |||||||| ||||| ||||
gtaagtctctctcactagtca----ctaataa---tacttagatcaaatttaaa-----tgatt-aacaatatttattacaaataaattgtgt---gaagCTATCATCTACCAACAATGAGCATGACGAGATAGACTTTGAGTTCCTTGGAAACAGAACAGGACAACCAGCTATATTACAGACAAATGTATTCACAGGAG
















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|192298568|gb|FG988524.1|FG988524
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192323920|gb|FK015671.1|FK015671
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|9203732|gb|BE329956.1|BE329956
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192296733|gb|FG993031.1|FG993031
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192308008|gb|FG998991.1|FG998991
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|21677268|gb|BQ629619.1|BQ629619
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|9898982|gb|BE607950.1|BE607950
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|18734985|gb|BM528499.1|BM528499
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192307523|gb|FK002041.1|FK002041
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192327911|gb|FK022456.1|FK022456
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192296130|gb|FG989490.1|FG989490
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
EST: gi|192324285|gb|FK018261.1|FK018261
EST:     ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTAT                         TTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG
genomic: ACATAAAGATGGTTCCTGGCGATTCAGCTGGCACAGTCACTGCTTTTTATgtatgcacaa ... aatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttcaaatttttgcttcaaccttgtttatttgctatgattggaatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGGAACAGAACAGGACAACCTTACATTTTGCAAACAAATGTGTTCACCGGAG
     tcaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaactttatactattaataatattctaattaaattatatatactagttttcaaatttttgcttcaaccttgtttatttgctatgattggaatcctatagTTATCTTCTCAAAATGCGGAGCACGATGAGATAGATTTTGAGTTCTTGGGGAACAGAACAGGACAACCTTACATTTTGCAAACAAATGTGTTCACCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatg