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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatatcttgaaaccaaatcaccagtccaccgcttactgaaaggaaaatagaaagagggagaaaaataatagatgcttgctggtgtattattacatgcacactatctttgcgttggtgttgatatatctaacatgatggattttgaatttggcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCAAGCACTGATGGAAAAATAATTCGTTATGCTGGGCCACAATACCCAACA

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 9
gttatatcttgaaaccaaatcaccagtcc---accgcttactgaaaggaaaatagaaag-agggagaaaaataatagatgcttgctggtgtattattacatgcacactatctttgcgttggtgt-tgatatatctaacatgatggattttgaatttggcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCAAGCACTGATGGAAAAATAATTCGTTATGCTGGGCCACAATACCCAACA
|| | |   | |   |   | ||| ||||     | |  | ||  | ||||| |||||  | | | ||| || | ||| |      |   | ||   | ||| | | | ||     |    ||  |  | |  ||||| |  | |||   |  || |   ||||||||| ||||| |||||||| || || ||||| |||||||||||||||||||| |||||||||||||  ||| |  |||||||| |||||    ||||||  
gtaaaaatatcatgtcgcttgacctgtcctgagtccccaagtgttatgaaaaaagaaaacatgaataaatatcaaagaagaaaagagagatgtttccagatg-agattttcagctggacaatgccttctgttgctaactt--ttgatgc-gccttcgttctgtccagAGAGTCCTCAATGGCGAGGCGAACTATGGCAGGCAAATTGTGACCATATCCAGCACTGATGGAAGGATAGTCAGTTATGCTTGGCCAGTGCACCCAAAT

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 9
gttatatcttgaaaccaaatcaccagtccaccgcttactgaaaggaaaatagaaagagggagaaaaataatagatgcttgctggtgtattattacatgcacactatctttgcgttggtgttgatatatctaacatgatggattttgaatttggcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCAAGCACTGATGGAAAAATAATTCGTTATGCTGGGCCACAATACCCAACA
      |    |||  |      || |  ||| |   |   ||| |  ||  |||    || || || |||| ||      |     |  |  |   | | ||| ||  || |||  |||||      ||||| ||||| || || |||     |||||||||| ||||| |||| ||| ||||| || || || ||||||||||||||||| |||| ||||||||||||||| ||||||||| ||||| |  ||||||| 
-----gtaaaaaaaatatcctgtcactttaccccagccaccaagtattatgaaaaa---gaaaacaagaataaata-----tcaaagaagaaaagggggatact-tcaatgtgttc-tgttg------ctaacttgatgcatcttcaat-----ttgtccagAGAGTCCTCAATGACGAGGCAAACTACGGCAGACAAATTGTGACCATATCCAGCATTGATGGAAAAATAATACGTTATGCTAGGCCAGATCACCCAACT
















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|29665229|gb|CB661504.1|CB661504
EST:     GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAG                         AGGGTCCTGAATGGCGAAGCAAATTATGGGAGGGCAA-TTGTGACCATATC
genomic: GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAGgttatatctt ... gcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGG-CAAATTGTGACCATATC
EST: gi|29628535|gb|CB633546.1|CB633546
EST:     GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAG                         AGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCA
genomic: GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAGgttatatctt ... gcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCA
EST: gi|2443121|gb|C74892.1|C74892
EST:     GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAG                         AGGGTCCTGAATGGCGAA-CAAATTATGGGAGGCAAATTGTGACCATATCA
genomic: GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAGgttatatctt ... gcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCA
EST: gi|3766939|gb|AU031049.1|AU031049
EST:     GTTNCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAG                         AGGGTCCTGAATGGCGAA-CAAATTATGGGANGCAAATTGTGACCATATCA
genomic: GTTGCAAAAAATCAGATAAAGGTCCTTGGAAGGATCCTAACATAATAAAGgttatatctt ... gcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgttggtgttgatatatctaacatgatggattttgaatttggcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCAAGCACTGATGGAAAAATAATTCGTTATGCTGGGCCACAATACCCAACA
                   atctaac  putative branch site (score: 2)
                                              cttgtcc  putative PPT
                                 attttgaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatatcttgaaaccaaatcaccagtccaccgcttactgaaaggaaaatagaaagagggagaaaaataatagatgcttgctggtgtattattacatgcacactatctttgcgttggtgttgatatatctaacatgatggattttgaatttggcttgtccagAGGGTCCTGAATGGCGAAGCAAATTATGGGAGGCAAATTGTGACCATATCAAGCACTGATGGAAAAATAATTCGTTATGCTGGGCCACAATACCCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG