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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaataatttgaactgtttaaaccgcattgcttttgaacagtttccgtttccccctgaggctgactatgttgcgttaccggttttgtatag

Basic information

species Zea mays
transcript GRMZM2G029396_T02
intron # 9
splice site 5'
intron type U2

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|32836193|gb|CD975871.1|CD975871
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGT
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGT
EST: gi|5791416|gb|AI978208.1|AI978208
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGGCTGCAGGAAGTTCGAAATTAC
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
EST: gi|5929059|gb|AW056351.1|AW056351
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGGCTGCAGGAAGTTCGAAATTAC
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
EST: gi|211268369|gb|FL477039.1|FL477039
EST:     ACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGGCTGCAGGAAGTTCGAAATTAC
genomic: ACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
EST: gi|113688993|gb|DW846079.1|DW846079
EST:     GTAAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGAC
genomic: GT-AGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGAC
EST: gi|60338190|gb|DN205163.1|DN205163
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGGCTGCAGGAAGTTCGAAATTAC
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
EST: gi|32838650|gb|CD978328.1|CD978328
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGT
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGT
EST: gi|113677732|gb|DW834544.1|DW834544
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGAC
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGAC
EST: gi|60399247|gb|DN232061.1|DN232061
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATG
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATG
EST: gi|86472947|gb|DY239317.1|DY239317
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTAC
EST: gi|6022598|gb|AW067410.1|AW067410
EST:     TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACANACTCTGCCAATCTG                         ATCCTTTTCGTACTCTGTAGT
genomic: TGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGT

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: 161

GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTACTGGCTGTAGAAGTGTAGATCATACGGCAGCATGCTACTGCTTCCATGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTACTGGCTGTAGAAGTGTAGATCATACGGCAGCATGCTACTGCTTCCATGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTACTGGCTGTAGAAGTGTAGATCATACGGCAGCATGCTACTGCTTCCATGAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 116

GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaa ... ttttgtatagATCCTTTTCGTACTCTGTAGTCCCCAATGACTGCAGGAAGTTCGGAATTACTGGCTGTAGAAGTGTAGATCATACGGCAGCATGCTACTGCTTCCATGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTCCTGCTGGTGGCTATCCTTTTCGGGGCACTGTATACCAAGTGACTTGTAGCTGGCCTTTTTCCCCTATGGAGACGAGACAAACTCTGCCAATCTGgtatggcaaataatttgaactgtttaaaccgcattgcttttgaacagtttccgtttccccctgaggctgactatgttgcgttaccggttttgtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA