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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatgggacatgtcacatatgcaccttatttaaggactgggtggggcagttgctcatctcttcttgattgtttccatttatgcttttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCAATGAACTGGGTATGATGGAGAATCAGTTGAGTCGATCAAAGGATGCAGC

Basic information

species Zea mays
transcript GRMZM2G341271_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341271_T05 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 9
gtagatgggacatg-tcacatatgcaccttatttaaggactgggtggggcagttgctcatc-------tcttcttgattgtttccatttatgct-tttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCAATGAACTGGGTATGATGGAGAATCAGTTGAGTCGATCAAAGGATGCAGC
|||||  |||| || |||||| |  | |||  |    |   || |||  ||  |  || |        |    |   || ||   | ||   || | |||| || |||||||||||| | ||||||||||||||||||||| |||||||||| ||  |||   || |||| |||||  ||| | |||| |||||||| ||
gtagagtggacctgatcacatttatagcttgctagctgg--ggatggctcatctcttcgtgaagagcgtaacataagtttttcttaattccactgtatagGGAAAAAAGACTTCAAGGACGAGATTCATGTTATGGCTGCATCACTCTCCAAAGAGATGGAATTGTTGGACAATCAAATGAATAGATCCAAGGATGCGGC
















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|22489980|gb|BU049903.1|BU049903
EST:     TGAAAAGAATGATCTTGAANCCAAGGTTGAGGAGACTTTGCAAGATTCAG                         GTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCA
genomic: TGAAAAGAATGATCTCGAAACCAAGGTTGAGGAGACTTTGCAAGATTCAGgtagatggga ... atgcttttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCA
EST: gi|31350903|gb|CD435260.1|CD435260
EST:     TGAAAAGAATGATCTCGAAACCAAGGTTGAGGAGACTTTGCAAGATTCAG                         GTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCA
genomic: TGAAAAGAATGATCTCGAAACCAAGGTTGAGGAGACTTTGCAAGATTCAGgtagatggga ... atgcttttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgggtggggcagttgctcatctcttcttgattgtttccatttatgcttttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCAATGAACTGGGTATGATGGAGAATCAGTTGAGTCGATCAAAGGATGCAGC
                           tcttgat  putative branch site (score: 4)
                                              tgctttt  putative PPT
                                         atttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatgggacatgtcacatatgcaccttatttaaggactgggtggggcagttgctcatctcttcttgattgtttccatttatgcttttagGTAAGAAAGACTTCAAGAATGAGATTCATGTTATGGCTGCAGCACTCTCCAATGAACTGGGTATGATGGAGAATCAGTTGAGTCGATCAAAGGATGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG