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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtttttgttttttgttctgtag

Basic information

species Oryza sativa
transcript LOC_Os12g13170.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 12
TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtt--tttgttttttgttctgtag
|||||| ||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| ||||| || || |||||||||| ||||| |||| ||||||||  || |   | | |||  | |  |  | | ||||| ||  ||  ||||||    |  | || ||| || | |||||
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTACGAGGAACTTCTATCAAGGAATAACTCACTAAAGgtt-agtctgcaacttttcaattt--tattctgctgaagtacgtatgttaacatctctgttctgctttctgctgtgtag

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G074373_T02 (Zea mays), 5'ss of exon 13
TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtt--tttgttttttgttctgtag
|||||| ||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| |||||||| || ||||||||||||||||  ||| |||||||| |   |   | | |||  | |  |  ||| ||||| ||| ||  ||||||    |  | || ||| || ||| |||
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgtt-gacctgcaacttttcaattt--tattatgctgaagtatgtatgttaacatctctgttctgctttgtgctctatag
















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|29629931|gb|CB634940.1|CB634940
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|86841957|gb|CI338364.1|CI338364
EST:     GTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|29626016|gb|CB631027.1|CB631027
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|29659468|gb|CB655743.1|CB655743
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|88548426|gb|CI476797.1|CI476797
EST:     GAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|86524936|gb|CI165142.1|CI165142
EST:     TGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACGTAACTGATGAGGCAGGAGTTGACAAT
genomic: TGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|88538158|gb|CI467164.1|CI467164
EST:     TATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: TATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|89193584|gb|CI116217.1|CI116217
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACCAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|25804027|gb|CA759988.1|CA759988
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
EST: gi|29676440|gb|CB672715.1|CB672715
EST:     GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAG                         GAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT
genomic: GGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttc ... tgttctgtagGAAAAACTTGAGGACAAACAACACAAAACTGATGAGGCAGGAGTTGACAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtttttgttttttgttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA