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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctctaaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaaattgtgaatgtctaattttaattttgattgtctttgtag

Basic information

species Glycine max
transcript GLYMA15G12980.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12980.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 5'ss of exon 7
CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctctaaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaaattgtgaatgtctaattttaattttgattgtctttgtag
|| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| ||  |||           ||      ||    | |    |    |  ||       ||  |   |||   ||  | | |   || ||  |||  |  |                                               
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcg--attaacttccaaatactgacctc-------acatttcagaaaaaga-aaagctcatggctgtttgtttctcgcag--------------------------------------------

upper sequence: GLYMA15G12980.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctctaaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaaattgtgaatgtctaattttaattttgattgtctttgtag
|| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| ||  |||           ||      ||    | |    |    |  ||       ||  |   |||   ||  | | |   || ||  |||  |  |   || |                                        
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcg--attaacttccaaatactgacctc-------acatttcagaaaaaga-aaagctcatggctgtttgtttctcgca-gacag---------------------------------------
















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|192303520|gb|FG994498.1|FG994498
EST:     TTGTTGGAGACTACCCAAAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
EST: gi|192305848|gb|FG995426.1|FG995426
EST:     CTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: CTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
EST: gi|193462959|gb|FK427724.1|FK427724
EST:     TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
EST: gi|17024037|gb|BM095071.1|BM095071
EST:     TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGC
genomic: TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGC
EST: gi|58016977|gb|CX703719.1|CX703719
EST:     TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
EST: gi|58016661|gb|CX703403.1|CX703403
EST:     TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: TTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
EST: gi|192305847|gb|FG995425.1|FG995425
EST:     CTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG                         ACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG
genomic: CTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgt ... gtctttgtagACTATCACACCTTTTCGTGGACACTTGGATTTCTCATTTGCATCTGCATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctctaaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaaattgtgaatgtctaattttaattttgattgtctttgtag

- - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA