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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCACACTGGTAGAGCCCCTAAGGGAGATCGAACTGATTGGGTTATGCATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaactttgactgaacaagcaagtgtgagttttgtagtgtttgtgactggatttctagtatagttgctacttcattgccctctgtttcactagaaa...

Basic information

species Glycine max
transcript GLYMA04G39140.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39140.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G64060.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTTCACACTGGTAGAGCCCCTAAGGGAGATCGAACTGATTGGGTTATGCATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaactttgactgaacaagcaagtgtgagttttgtagtgtttgtgactggatttctagtatagttgctac-ttcattgccctctgtttcactagaaa
|| ||||   || | |   |||   || ||||| ||||||||||| || ||||||| ||||||||| ||||| || |||||| |  |    ||    |||||||       ||||    |   |  || |   |||| ||  |||| ||| |   || | ||| || |    |   |  |||  | |||            
TTATCACTACGGGAAAATACCTCGCGGTGATCGGACTGATTGGGTCATACATGAATATAGACTTGAAGACAAAGTACTGGCTCAAAAGAATGTTCCTCAGgtaa-------tgacgattcgttcttgtct---ttttttaacgttt-tgattcc-ttgcaagtttactaaacatgcttgttgtgccctgcag---------
















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|19268804|gb|BM885060.1|BM885060
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
EST: gi|208050164|gb|GD849475.1|GD849475
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
EST: gi|193322050|gb|FK284884.1|FK284884
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATT
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATT
EST: gi|208170537|gb|GD967420.1|GD967420
EST:     TGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATTTGTAGGGTGTACCAAAAGGGAGGGTCCTGGTCCTAG
genomic: TGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATTTGTAGGGTGTACCAAAA-GGAGGGTCCTGGTCCTAG
EST: gi|208273966|gb|GE071462.1|GE071462
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
EST: gi|207689205|gb|GD672690.1|GD672690
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATAGTAAGATTTGTAGGGTG
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTAT-GT--GATTTGTAGGGTG
EST: gi|298196620|gb|HO041363.1|HO041363
EST:     ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAG                         GACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG
genomic: ATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaact ... tgtattgtagGACTCCTATGTGATTTGTAGGGTGTACCAAAAGGAGGGTCCTGGTCCTAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCACACTGGTAGAGCCCCTAAGGGAGATCGAACTGATTGGGTTATGCATGAATTTAGACTTGATGACAAGGTGCTGGCTGATGAAGGCGTATTGCAGgtaaacaactttgactgaacaagcaagtgtgagttttgtagtgtttgtgactggatttctagtatagttgctacttcattgccctctgtttcactagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctgt