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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagcatcattagtttcaataatatttgttagcttctggattgtagttaattcacggggtatcttgttttcaagtgtttgtttcaatgtatgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC

Basic information

species Oryza sativa
transcript LOC_Os09g24650.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 9
-gagcatcattagt-ttcaataatatttgttagcttctggattgtagttaattcacggggtatcttgttttcaagtgtttgtttcaatgta-tgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC
  | || | |  ||  |   |  |   || ||  | ||| ||  | ||| |      |||  | || | |  || |   |  ||   | |  ||| ||| |||||||| |||||  |||| ||| | |||||||||||||| || ||||| || |||||||  ||||||||||||||||| |||||||| || ||| ||||||
gcatcaccttccgtgcttccttgttactgctatttactgcatc-tggttcagctctagggccttttatat--aaatccctaattacgtatggtgtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G113619_T02 (Zea mays), 3'ss of exon 9
gagcatcattagtttcaataatatttgttagcttctggattgtagttaattcacggggtatcttgttttcaagtgtttgtttcaatgta-tgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC-------
   | ||  |  || |  |  |   || ||  | ||| ||  | ||| |      |||  | || | |  || |   |  ||   | |  ||| ||| |||||||| |||||  |||| ||| | |||||||||||||| || ||||| || |||||||  ||||||||||||||||| |||||||| || ||| ||||||       
---cttccgtgcttcc--ttgttactgctatttactgcatc-tggttcagctctagggccttttatat--aaatccctaattacgtatggtgtctgtccaggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACACCACAGCA
















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|86431015|gb|CI083438.1|CI083438
EST:     AGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATACATTCTTCAGTCTGGG
genomic: AGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|38471428|gb|CF955559.1|CF955559
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|86831029|gb|CI295513.1|CI295513
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88982076|gb|CI027653.1|CI027653
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|29626393|gb|CB631404.1|CB631404
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTTTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|218496676|gb|FG944369.1|FG944369
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCTGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88223285|gb|CI223134.1|CI223134
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|16575403|gb|BI802699.1|BI802699
EST:     CTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: CTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattcacggggtatcttgttttcaagtgtttgtttcaatgtatgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC
 agttaat  putative branch site (score: 4)
                                              tttgttc  putative PPT
                 ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagcatcattagtttcaataatatttgttagcttctggattgtagttaattcacggggtatcttgttttcaagtgtttgtttcaatgtatgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA