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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgaaaataaaaacttatattcctgtagcaagttcatgttggtatgtatatggttcaaaattgcataaaatctggctaattacattatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT

Basic information

species Zea mays
transcript GRMZM2G050658_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050658_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g13870.3 (Oryza sativa), 3'ss of exon 4
---------gtaagatgaaaa--taaaaacttatattcctgtagcaagttcatgttggtatgtatatggttcaaa---------------------attgcataaaatctggctaattacattatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT
          || | | ||||  ||||      | ||| |  |||| |||  ||||| | |    ||  ||||||                     | || |  | | ||  || |      |   ||  |||||||||||||  | ||||||||||| |||||| |||||| |||||| || ||||| ||||| |||||||||||||| || || |||  |||||
gtaaggttcttaggctaaaaacctaaagtgcacttttcttcaagcatgtttgtgttgatcttctcattattcaaatgttttatctttctgagtcttagtggaccagaactcactgaaggaccttctttccagGTTTATGATAATGTCACTACTGGTGTCATATGCCATGGAGAGAAGAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT
















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|32851915|gb|CD991596.1|CD991596
EST:     GACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGCTATATGCAATGGAGTGAAGAGCGTA
genomic: GACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
EST: gi|38229749|gb|CF920062.1|CF920062
EST:     GACGGCCTCNTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
genomic: GACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
EST: gi|211132096|gb|FL293580.1|FL293580
EST:     TCTGGCGCTGTTTCCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
genomic: TCTGGCGCTGTTTCCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
EST: gi|13178326|gb|BG349584.1|BG349584
EST:     CCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
genomic: CCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
EST: gi|13178327|gb|BG349585.1|BG349585
EST:     GTTTCCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
genomic: GTTTCCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
EST: gi|86471570|gb|DY237940.1|DY237940
EST:     TTTCTGGCGCTGTTTCCCTAATGGAAATGAGT                         -TTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGT
genomic: TTTCTGGCGCTGTTTCCCTAATGGAAATGA-Tgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGT
EST: gi|34391242|gb|CF384470.1|CF384470
EST:     GACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGAT                         GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA
genomic: GACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAATGGAAATGATgtaagatgaa ... tatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatgtatatggttcaaaattgcataaaatctggctaattacattatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT
                                 ggctaat  putative branch site (score: 3)
                                            ttatcttt  putative PPT
                                    taattacattatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgaaaataaaaacttatattcctgtagcaagttcatgttggtatgtatatggttcaaaattgcataaaatctggctaattacattatctttaagGTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA