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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatgacatgcagtcatttcttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg...

Basic information

species Glycine max
transcript GLYMA20G02950.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgt--tatatgttttcaaattttaaaa---atgacatgcagtcatttcttacaattttggcta-gattattttgtctctattcattctgtaatgcttaaataaactg
| |||||||||||||||| || || ||||||||||||   ||||| ||||| || | |||||||||||| || ||  | ||| | |||||  |     ||||||    ||        | |  |  ||     |  |    || ||  |     | ||    ||  ||  | | ||   ||| | |  | || |
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgtgcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag

upper sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
lower sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 13
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatgacatgcagtcatttcttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg
| | |||||||||||||| |||||||||||||| |||   ||||| | ||| || ||||||||||||||||| ||  | ||  | |||||  ||||| |      | |  |       |   ||      ||  || ||        || | |||| |  | || | | |                  
GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAGgtagtatgtcta-----tctgcatgccctttctggttgcaggttctaaattctaactctttctgttgtttacactcgtgcag------------------

upper sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 13
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatgacatgcagtcatttcttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg
||| |||||||||||||| || |||||||||||||||   |||||   ||| || ||||||||||||||||| ||  | ||  | |||||   | ||     || | ||    |  |||||  |   |  || ||  ||   ||| |||       | || |   || | || ||||    |  |   
GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAGgt---aggt-----aactctac---ttgcatgccctttctgtttgcaggtt---ctaaatt---ccaaccctttctgttgttta-tgctctcgtgcag--

upper sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatga--catgcagtcattt-cttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg
| ||||||| |||||||| ||||| ||||||   ||| ||||||| ||||| || |||||||||||||| || ||||||||||||||||| |       | |  || | | | ||   |||| | |||||   ||| |||  |||  | |  | |  | ||     | ||   ||    || ||      |
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacg-accataatgttcttacattggatcatgtattcattggtttataataatggtgacacgact--gccttgcacctttaactagcttttgaactggtag

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|21601739|gb|BQ612070.1|BQ612070
EST:     TGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG                         GTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA
genomic: TGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgtt ... ttttgaacagGTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA
EST: gi|213602617|gb|DB978088.1|DB978088
EST:     AGATAGGAGTTTGAAG                         GTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA
genomic: AGATAGGAGTTTGAAGgttatatgtt ... ttttgaacagGTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA
EST: gi|51344791|gb|CO985524.1|CO985524
EST:     TGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG                         GTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA
genomic: TGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgtt ... ttttgaacagGTCAAGTTAAGATGCGGGTTGAAAAACGAGATTACTGATGTAGATGAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatgacatgcagtcatttcttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG