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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAGAATCCAAGCAATACCAGATGGGGCTCCTCCTGTGCCAAAACAAACTGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagttatccatgtctcaggctgatgcaattatcgtatttcatctgtgagaggccttttaaataactgactctgttcatgtatgtgaatcactgaatcatctcaaatatag

Basic information

species Glycine max
transcript GLYMA10G05870.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05870.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 5'ss of exon 3
GATAGAATCCAAGCAATACCAGATGGGGCTCCTCCTGTGCCAAAACAAACTGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaa----tctagt--------tatccatgtctcaggctgatgcaattatcgtatttcatctgtgagaggccttttaaataactga------ctctgttcatgtatgtgaatcactgaatcatctcaaatatag-----
||||| |||||||||||||||||||||||| |  |||  || |||||||||||||| ||||||||||| ||||| ||| | ||||| || |||||||||||| |    ||  ||        |||| |||| |  |  |       |||| ||| |     | | |      || ||||| | ||        ||  || |||  ||    ||||| |    | ||| ||  |      
GATAGGATCCAAGCAATACCAGATGGGGCTGCAACTGCACCCAAACAAACTGGAGGTTGGGCAGCTTCAGCTTCTCGTACAGAAATCAAATTTGATTCAGgtgactgttcatgtagagattgtatctatgtattggattttgagtcttatggtaatgtggtt-tcattatttttctaaatgagtggaatgctttcaattaatgcttgcagttcacttatatgtttcacatgaatgatag
















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|209719210|gb|BW679776.1|BW679776
EST:     TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAG                         ATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
genomic: TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagt ... tcaaatatagATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
EST: gi|26048180|gb|CA784745.1|CA784745
EST:     TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAG                         ATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
genomic: TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagt ... tcaaatatagATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
EST: gi|18730524|gb|BM525925.1|BM525925
EST:     CACGTCCTGAAATTAAGTTTGATTCAG                         ATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
genomic: CACGTCCTGAAATTAAGTTTGATTCAGgtaatctagt ... tcaaatatagATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
EST: gi|298198162|gb|HO039701.1|HO039701
EST:     TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAG                         ATGGGCGATTTGATGATGAATACTT
genomic: TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagt ... tcaaatatagATGGGCGATTTGATGATGAATACTT
EST: gi|26048411|gb|CA784901.1|CA784901
EST:     TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAG                         ATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT
genomic: TGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagt ... tcaaatatagATGGGCGATTTGATGATGAATACTTCCAACAAAGTGAACAATCAAATCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAGAATCCAAGCAATACCAGATGGGGCTCCTCCTGTGCCAAAACAAACTGGAGGCTGGGCAGCTTCTGCTTCACGTCCTGAAATTAAGTTTGATTCAGgtaatctagttatccatgtctcaggctgatgcaattatcgtatttcatctgtgagaggccttttaaataactgactctgttcatgtatgtgaatcactgaatcatctcaaatatag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT