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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACTTCGATTTCGGCCTCGACGGCGAAGGCGCCTTCGATGCCCTCGGCGAGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccctcgttcatttccttcaatcaatccctcattcgttttcttcattcacgaaaccctttctcagttaaatttgaaacgcag

Basic information

species Glycine max
transcript GLYMA20G16170.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16170.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 5'ss of exon 1
TGACTTCGATTTCGGCCTCGACGGCGAAGGCGCCTTCGATGCCCTCGGCGAGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagt--cc--------ctcgttcatttccttcaatcaatccctcattcgtt-ttcttcattcacgaaaccctttctcagttaaatttgaaacgcag--------------------------------------------------------------------------------------------
 || ||||| |||||    || || ||||||||||| |||||| |||| |||||||||||||| || || |||||   |||||||    | ||||| |  || |||  ||        || |||  ||  |||   ||| | |     ||||  ||||  ||||     | | || ||   ||  ||||                                                                                                     
GGATTTCGACTTCGGTGAGGAAGGTGAAGGCGCCTTTGATGCCGTCGGTGAGCTCCTCGTCGCTGCTGAATGCGTTTCCGATTTCGAAGAGTGCCGTTTGgtaagtaaccattcgcagcttgttgcttggctttcttcatttcaattatcgtaattctagattcgttttatctttgcttgtttgtatttatgggattttttcgttagggcctctgtgactgttgaaatggtttcaataaggtctcgcttttgaatgagctgagatatttaattggatgtggtgtgtgtag

upper sequence: GLYMA20G16170.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 5'ss of exon 1
TGACTTCGATTTCGGCCTCGACGGCGAAGGCGCCTTCGATGCCCTCGGCGAGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccctcgt--tcatttccttcaatcaatccctcattcgttttcttc-attcacgaaaccctttctcagttaaatttgaaacgcag----------
|||||||||||||||| || | |||||||||||| |||| ||| |||| || |||||||| | | |||  ||||||  ||||  | |  | |||||||| ||  || | |  |  || |||| ||   |   | || | ||   | | ||  | || || ||    |  ||  |||| || |||                
TGACTTCGATTTCGGCTTCCAAGGCGAAGGCGCCGTCGACGCCATCGGAGAACTCCTCGTTGACTCCGGATGCGTCTCCGATGACGCTGAATGCCGCTCTgtacgttctttttcttcgtttcgtttttttttttccgcttttaatctattggactctcgtaaattatcatcgcttaatttcgaatttttttagtttctag
















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|213617333|gb|DB965204.1|DB965204
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|213598692|gb|DB958192.1|DB958192
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|209701446|gb|BW655827.1|BW655827
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|213603604|gb|DB966774.1|DB966774
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|23725561|gb|BU760739.1|BU760739
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|9987507|gb|BE661615.1|BE661615
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|213589815|gb|DB959426.1|DB959426
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
EST: gi|209716195|gb|BW668695.1|BW668695
EST:     AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCC                         GTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG
genomic: AGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccct ... tgaaacgcagGTATGCAGCACGCTGTGCGACAAGTTCGGGAAGCACGGTTTGGTGAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACTTCGATTTCGGCCTCGACGGCGAAGGCGCCTTCGATGCCCTCGGCGAGCTCCTCGTCGCCGCCGACTGCGTCGACGATTTCTCCCACTGCCGCTCCgtgagtccctcgttcatttccttcaatcaatccctcattcgttttcttcattcacgaaaccctttctcagttaaatttgaaacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC