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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgaatattcccatgctgttttttgtgctgtattacctgattgatagaaagcatggttgaactctgtacataaaattaattacttgaacttattacagGTCTCGAACCAGTTGAACAAACTGTACATGAAATTTCTAAAGAGAAATCCTGGTTACAGTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G318860_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G318860_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 3'ss of exon 9
--acatgaatattcccatgctgttttttgtgctgtattacctgattgatagaaagcatggttga-actctgtacataaaattaattacttgaacttattacagGTCTCGAACCAGTTGAACAAACTGTACATGAAATTTCTAAAGAGAAATCCTGGTTACAGTGGAAAG
  |  ||    ||||  | |||||        |  ||      | |||  | ||||||  ||   ||||  || |||||||| |  | || |   |   ||||||||| |||||||||||| |  ||||||  || ||| | ||||||||||||||||| |||||||||
ttatgtgccatttcctgtactgttcaaaaattttgatcgt---aatgactggaagcatattttttactcgttatataaaattgaggatttaagtctgcaacagGTCTCAAACCAGTTGAACCAGTTGTACACAAAGTTTATCAAGAGAAATCCTGGTTATAGTGGAAAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaaagcatggttgaactctgtacataaaattaattacttgaacttattacagGTCTCGAACCAGTTGAACAAACTGTACATGAAATTTCTAAAGAGAAATCCTGGTTACAGTGGAAAG
                              aattaat  putative branch site (score: 3)
                       tacataaaattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgaatattcccatgctgttttttgtgctgtattacctgattgatagaaagcatggttgaactctgtacataaaattaattacttgaacttattacagGTCTCGAACCAGTTGAACAAACTGTACATGAAATTTCTAAAGAGAAATCCTGGTTACAGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA