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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaag

Basic information

species Glycine max
transcript GLYMA13G00980.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00980.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 5'ss of exon 12
GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaag
|| || |||||  | || || |||||||| |||||||||||||||||||||||  | || || ||| | ||||||||||||        ||  | |    | |  ||||||||||  ||  |   |    |||  ||    | || | | ||||  |  ||  |  ||      || | |   |||
GATGTCTTTGATTTGCCGTTCCACATGGCTAGAGATCAAATAGAAGAAAGTCTCAGAAATAAGATGACCTCTATAAAGgtag------gttgtttttttctacatatttttatctcatat-ttcctattgataacaaaacctagactttttttg--taatatttatttttctgctgtatttgaaag

upper sequence: GLYMA13G00980.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S145_44V6.1 (Physcomitrella patens), 5'ss of exon 12
GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattacttattagtatcac--tttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaag
|| ||||||||||| || ||||||||||| ||||||||||| ||| ||||| | |||   |||||| ||  ||| ||||| |  | || | | | | ||     |||     ||| ||||      |||  ||| | |  |    || |   | |  ||   ||    |  | || | |||   |   
GATGTATTTGACCTACCGTTTCACATGGCTAGAGATCAAATTGAACAAAGTTTACGTGCTAAAATGTCTATTATCAAGgtgag-aattgtcactcttacaacccccagcagctatattttggactgttg--tattttaccg--ccgaatacttct--ttagaaagaaataaacaagtaaaacgag---

upper sequence: GLYMA13G00980.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S47_178V6.1 (Physcomitrella patens), 5'ss of exon 12
GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattacttattagta--tcactttccaatttttatcttttaagtatttgcatat-atgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaag
|| ||||||||||| |||||||| ||||| ||||||||||| ||| ||||| | |||  ||| ||| |  |||| |||||||     |   ||    || | |   |     || || ||      ||   | | |  |  |||    || ||  |    | |||   |  ||||| | |         
GATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAGgtaagagtgttgcagctcctcccctattaccagatagctcttggtacgttatgttttaccaccgaacctcttctcaataagagataat--ccagaaaaataa---------

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|10236681|gb|BE805569.1|BE805569
EST:     CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG                         GAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
genomic: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattactt ... aaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
EST: gi|51344846|gb|CO985579.1|CO985579
EST:     CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG                         GAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT
genomic: CCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattactt ... aaatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAGgtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattgaaatatgaag

- - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - -  AAGAAA