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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcag

Basic information

species Zea mays
transcript GRMZM2G074790_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 5'ss of exon 12
CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaagattt---tagaaagtgatatttgtgtgaagttccttttccagtctt-----cttcagtatgtgcatgtaaagtgcag
|||||||||||||| |||| ||||||||||||||| |||||||||||||| ||||| ||| |||| ||||||||||| ||||||||||| ||||||||||||||   ||    |  | |||||| |||   || | ||| ||| ||    ||       |||| || | ||| |  | |||||
CTTAGAGAATCAATGGACAAAAGCACTGCTGTATTTGACAAAGAAAAGGCTCAAGAACGTCTATCAAAGTTATCTGGTGGTGTTGCTGTCCTCAAGgtttgttatttttcaggtgcacagtgatgtttcactgtatttcttttccccactttgctcctctcaggatatccattttgactgcag
















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|67028320|gb|CO457069.1|CO457069
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|166512699|gb|EG211950.1|EG211950
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTG
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTG
EST: gi|76911014|gb|DV164129.1|DV164129
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|211181730|gb|FL012621.1|FL012621
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAGGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|211184128|gb|FL012625.1|FL012625
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGNNNNNNNGATAGGGTGAC
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAG-AAAAAAGATAGGGTGAC
EST: gi|31352804|gb|CD437161.1|CD437161
EST:     AGGCTCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 400

CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG