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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatcaatttcctactgactatag

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 12
CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatcaatttcctactgactatag----------
|||||| ||||||| ||||| ||||||||||| ||||| || ||||||||||| || |||||||||||||||||||||||||||| | | || | |||  ||| | |||| | |||||| |    ||  ||||   |||  || ||  | |||                
CTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAGgtagcaaggcagctcttattttattctctat-aataatcacgtactattcca--tcatttatctctaaatgatagcttcttaatttag
















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|67028781|gb|CO457530.1|CO457530
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACATCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GGAC-TGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagG-ACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGA
EST: gi|211104642|gb|FL379460.1|FL379460
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|13125955|gb|BG316630.1|BG316630
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|32849483|gb|CD989164.1|CD989164
EST:     CACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCACTACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCA-TACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|60291876|gb|DN190115.1|DN190115
EST:     TTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: TTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA

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: 107

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 171

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatcaatttcctactgactatag

- - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA