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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCTGGAATACTTGGGATTTGGCTTAGTGGAGGTGTTGCTGTTCCGCTTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttgaaatccctattcttgcatttgttaatcattttggatggcttgcaaactttatgaagcccaggcctccttaatcagcccttgaatttgtct...

Basic information

species Glycine max
transcript GLYMA07G02180.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G02180.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 5'ss of exon 3
TGTTGCTGGAATACTTGGGATTTGGCTTAGTGGAGGTGTTGCTGTTCCGCTTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttgaaatccctattcttgcatttgttaatcattttggatggcttgcaaactttatgaagcccaggcctccttaatcagcccttgaatttgtct---
||||||||||||||| || | |||| |||||||||||||||| ||||| ||||||   |||||||||||||  ||||||||  ||||||| ||| |||||||  ||  |||| |  ||  ||||  ||||  |  |   ||||  ||  |   |||    ||  ||  || |  |      |   | | |    ||||     
TGTTGCTGGAATACTAGGAACTTGGTTTAGTGGAGGTGTTGCAGTTCCACTTGCACTTAGCTATCCAGAAGCTGAGCTCTTACATGTGATGAATGATTCGgttcgccctgaatttact-ctcttttattttcttgtatatttgagtgtttatgaaag--gatccagttcatgtttagcactttgtctcatattgttgttgaga
















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|11687559|gb|BF595235.1|BF595235
EST:     CAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCG                         GATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC
genomic: CAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttg ... ttggctgtagGATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC
EST: gi|11275001|gb|BF325325.1|BF325325
EST:     TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCG                         GATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATG
genomic: TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttg ... ttggctgtagGATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATG
EST: gi|254322525|gb|GR837939.1|GR837939
EST:     TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCG                         GATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC
genomic: TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttg ... ttggctgtagGATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC
EST: gi|21889136|gb|BQ742349.1|BQ742349
EST:     TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCG                         GATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC
genomic: TTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttg ... ttggctgtagGATGTATCTGCAATACTGAGTACTGAGGATCATACTGAAATAATGCAAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCTGGAATACTTGGGATTTGGCTTAGTGGAGGTGTTGCTGTTCCGCTTGCAACCAGCTATCCAGAAGTAGAGCTCTTGTATGTGATTAATAATTCGgtatgctttgaaatccctattcttgcatttgttaatcattttggatggcttgcaaactttatgaagcccaggcctccttaatcagcccttgaatttgtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT