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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaatcaattatgaacatattattgccttgctttcatttagagaaagttcagcaatattcagattggtttgggttatctattacag

Basic information

species Glycine max
transcript GLYMA16G05140.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05140.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g16940.1 (Oryza sativa), 5'ss of exon 3
ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaatcaattatgaacatattattgccttgctttcatttagagaaagttcagcaatattcagattggtttgggttatctattacag
||||||||||| || || || ||||||||||| ||||| ||||||||||| || || || ||||| ||||| | |||     || |        ||||| ||    |    | ||  | |  | |       | || |  || |     || | | ||    ||| |  ||                 
ATAATATACCTTGGGAAGCCAGATGGGCCTACTTGCCATACAGGGGCAGAGACTTGTTACTATACTTCAGTCTATGATGCTCTACAAGGTTCGAAGgtatctgttcttgggt-tgccctttctgtaaatgaacctttacatataa----tttaactatg---agactccttcacag------------

upper sequence: GLYMA16G05140.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G082214_T01 (Zea mays), 5'ss of exon 3
ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaatcaattatgaacatattattgccttgctttcatttagagaaagttcagcaatattcagattggtttg-ggttatctattacag
||||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| || |||||||| ||||||| |||     || |      | |||||          ||||| ||  ||   || | |    |  | || ||          ||  ||| | |||    |  | ||  |  | ||||
ATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAGgtactc-------attattaagttacactttcttgaaatagactttgact--------cataattaaaattaacatatgatttcccttcacag

upper sequence: GLYMA16G05140.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0068g00910.t01 (Vitis vinifera), 5'ss of exon 3
ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgta---acttcaatcaattatgaacatattattgccttgctttcatttag-agaaagttcagcaatatt----cagattggtttgggttatctattacag----------------
||||||||||| || || ||||| |||||||| |||||||| ||  | ||||| ||||||||| ||||||| ||||| ||||||||  | |   ||||    | | |  ||  |||||    | || |||  ||| |||  ||||| || |||  ||  ||| ||    |||      || ||  ||   ||| |                 
ATAATATACCTTGGGAAGCCTGACGGGCCTACTTGCCACACTGGATCTGAAACTTGCTATTATTCATCAGTATTTGATTTGTTAAAAAATCCTCAGgtttatattcctttcttttatggtattctttttgttttgtttttctttagtaggaagaacaataattttttcccagccctactttggacatgctttatattaattttttgttgcag

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|192295469|gb|FG987083.1|FG987083
EST:     CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG                         GCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
genomic: CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaa ... tctattacagGCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
EST: gi|26058540|gb|CA801454.1|CA801454
EST:     CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG                         GCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
genomic: CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaa ... tctattacagGCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
EST: gi|11413772|gb|BF425783.1|BF425783
EST:     CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG                         GCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
genomic: CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaa ... tctattacagGCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
EST: gi|19934822|gb|BQ079852.1|BQ079852
EST:     CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG                         GCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
genomic: CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaa ... tctattacagGCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
EST: gi|23056166|gb|BU577706.1|BU577706
EST:     CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG                         GCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA
genomic: CAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaa ... tctattacagGCTGAGGAAAATAAATTGGCATTAACCTCTTTGTATGCATTAGAGTCAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAGgtaacttcaatcaattatgaacatattattgccttgctttcatttagagaaagttcagcaatattcagattggtttgggttatctattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA