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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcctctgaataatcttatggatttatttgggatccacctatgatgatctagacttcaacttttatgtgtactcccaactcaagggttcctatgctcctagGTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCTAAGATTCTCAAGGGTGAAGTTGAAGGGACCAAATTCTACTTTCCTGTCG

Basic information

species Glycine max
transcript GLYMA19G39560.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G39560.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0104g01480.t01 (Vitis vinifera), 3'ss of exon 10
gtatttcctctgaataatcttatggatttatttgggatccacctatgatgatctagacttcaacttttatgtgtactcccaactcaagggttcctatgctc-ctagGTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCTAAGATTCTCAAGGGTGAAGTTGAAGGGACCAAATTCTACTTTCCTGTCG
|||    || | || || | | |   ||| |   | |   ||||  ||| |   |  ||||  || |||  |||  | |  | |  |  | ||   ||||  |||||| |||||||||||||||||||| || || ||||||||||| || |||||||| ||||||||  |||||| ||| ||||| ||||||  ||||||||| |
gtaacatct-taaacaaccatct---tttctgaagaacttacct--gat-actcaaccttc--ctcttacctgtcatgcacattttaaagatcaggtgcttgctagGTAATTGTATCATGGAATGGACTTGCTATTTCATCTTTTGCAAGAGCTTCTAAAATTCTCAAAAGTGAAGCTGAGGGGACTAAATTCCGCTTTCCTGTTG
















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|15815146|gb|BI787421.1|BI787421
EST:     AGTTGTTTGAAGTAAGGTCAAGGCGTCCAAAGCCACATTTGGATGATAAG                         GTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCT
genomic: AGTTGTTTGAAGTAAGGTCAAGGCGTCCAAAGCCACATTTGGATGATAAGgtatttcctc ... atgctcctagGTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctagacttcaacttttatgtgtactcccaactcaagggttcctatgctcctagGTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCTAAGATTCTCAAGGGTGAAGTTGAAGGGACCAAATTCTACTTTCCTGTCG
                                        ttcctat  CT-rich tract
           aacttttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcctctgaataatcttatggatttatttgggatccacctatgatgatctagacttcaacttttatgtgtactcccaactcaagggttcctatgctcctagGTTATTGTATCATGGAATGGACTGGCAATCTCATCTTTTGCTAGGGCTTCTAAGATTCTCAAGGGTGAAGTTGAAGGGACCAAATTCTACTTTCCTGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG