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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGAATTCTTTTGAGGATGTGAGCGACAAAGTAGTGGCTGACTTTGGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgcatctttccctgcttactttttcggggatcttgattttctttttgtttccgattccctatgttaccagaatcatagctgagattagaatcac...

Basic information

species Glycine max
transcript GLYMA01G34690.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G34690.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAGAATTCTTTTGAGGATGTGAGCGACAAAGTAGTGGCTGACTTTGGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgcatctttccctgcttactttttcggggatcttgattttctttttgtttccgattccctatgttac-cagaatcatagctgagattagaatcac--
|| |||||||| ||||  || |||||  |||| ||||||||||| ||||| || || |||||||| || ||||| |||||||| || ||| |||| |||||||| | ||   |   |||  | ||||      |  |  |    ||||  | |||  | | | | |   || |||    |||        |      ||  
GCGGAGAATTCATTTGGTGACGTGAGTAACAAGGTAGTGGCTGATTTTGGTTGTGGGTGTGGTACTTTGGGTGTGGCAGCTGCTCTCTTGGGTGCTGAgtgagtagtatagcttt-tgcccatttttctttctacttcaacc--ctttaagcttcataatacttttaagactcagccctataaagctacatgcccctaccc
















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|192324313|gb|FK018289.1|FK018289
EST:     GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGA                         ACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
genomic: GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgca ... cattgatcagACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
EST: gi|208334925|gb|GE132870.1|GE132870
EST:     GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGA                         ACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
genomic: GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgca ... cattgatcagACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
EST: gi|208125644|gb|GD920674.1|GD920674
EST:     GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGA                         ACATGTTCTTGGCATTGGCATTGATCCAGAATCTCTTGAAATAGCTTCCAA
genomic: GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgca ... cattgatcagACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
EST: gi|192328952|gb|FK019679.1|FK019679
EST:     GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGA                         ACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA
genomic: GGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgca ... cattgatcagACATGTTCTTGGCATTGACATTGATCCAGAATCTCTTGAAATAGCTTCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGAATTCTTTTGAGGATGTGAGCGACAAAGTAGTGGCTGACTTTGGATGCGGTTGTGGTACGTTAGGTGTTGCAGCTGCACTGTTGAGTGCAGAgtgagttgcatctttccctgcttactttttcggggatcttgattttctttttgtttccgattccctatgttaccagaatcatagctgagattagaatcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC