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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattgtctttcttactcattgtcggcaatttgctattttttctgaacacatatgttgtgttcaaagtctgctatcaagtaaatatgaaacagttt...

Basic information

species Zea mays
transcript GRMZM2G408989_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 3
CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattgtctttcttactcattgtcggcaatttgctattttttctgaacacatatgttgt----gttcaaagtctgctatcaagtaaatatgaaacagttt
|||| || || |||||||||||||||||||| |||||||| || || |||||||| ||||||||||| ||||| |||||||||||||| |||||||| |||||||  ||   |  |  ||    | |   | ||    ||||| | |   |  | | | ||      |    ||   || |  |   | |   |  ||| |   
CGATTTACTTGGAGGCAGTGGCAATTCTCCCTCAGTTAGTTTTGCTGCAGAGAAGTAGAAATGTGGACAACTTGACTGGACAATATGTATTCTTCCTAGGgtatgagtt--ttaccacacaagctttttaccataacatatttatacatgattcctgtattacaagagaatgaaacatgtttgcttttcatgcttcaacggc--
















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|16920990|gb|BM074929.1|BM074929
EST:     TGTTATCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: TGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     GTGGATAACTTAACTGGACAATATGTTATCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: GTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|32835284|gb|CD974962.1|CD974962
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     GCAGAAATGTGGATAACTTAACTGGGCAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: GCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattgtctttcttactcattgtcggcaatttgctattttttctgaacacatatgttgtgttcaaagtctgctatcaagtaaatatgaaacagttt

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