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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctcttcttttctatatattatatgggttgattatttatatttttctgtagaaagatagctagtttttcttttgaaattaatattattattgtga...

Basic information

species Oryza sativa
transcript LOC_Os08g32620.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G871463_T01 (Zea mays), 5'ss of exon 2
CAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctcttcttttctatatattatatgggttgattatttatatttttctgtagaaagatagct-agtttttc---ttttgaaattaatattattattgtga
|||||| |||||||||||||| |||||||| ||| |||| ||||| ||| ||||||||| |||| ||||||||||   |||| |||| | |||||||||||| ||    || |||  | | ||| ||||   |||  |||||   ||| ||   | ||   || || | | |||    | |  || ||| |    | |   |  
CAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaattgtttgttctttat-atattt-ttgggtattttcttttctccaaacaagtttaccttaatattttgagtctctaagttatttggttcaacct--
















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|33801423|gb|CF326583.1|CF326583
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|88478431|gb|CI415702.1|CI415702
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|88485934|gb|CI423205.1|CI423205
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAA-CTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|88845520|gb|CI084445.1|CI084445
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|88508474|gb|CI435980.1|CI435980
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|86508991|gb|CI151624.1|CI151624
EST:     CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: CAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
EST: gi|55408400|gb|CV720776.1|CV720776
EST:     GTTCAACAAAGTATGAGCCTAAG                         GCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG
genomic: GTTCAACAAAGTATGAGCCTAAGgtgagcctct ... tgaatggtagGCTGAGTCAAAAAGGCAGAGGAGGTGAAAACTCTTGACTGGGTAACATCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctcttcttttctatatattatatgggttgattatttatatttttctgtagaaagatagctagtttttcttttgaaattaatattattattgtga

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA