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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTCCTCGCGATTGATGTTTGGGAGgtatagttttgacattgtacttttcctttcctttcgttttcataaagtttacatctttactaacaattatcttcacttccggggacag

Basic information

species Zea mays
transcript GRMZM2G042080_T01
intron # 6
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|211285315|gb|FL458633.1|FL458633
EST:     ATGTTTGGGAG                         CATGCATACTATCTGGATTACGAG
genomic: ATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG
EST: gi|60348098|gb|DN215071.1|DN215071
EST:     CCACTCCTCGCGATTGATGTTTGGGAG                         CATGCATACTATCTGGATTACGAG
genomic: CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG
EST: gi|5439233|gb|AI820154.1|AI820154
EST:     ATTGATGTTTGGGAG                         CATGCATCCTATNTGGATTCCNAG
genomic: ATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG
EST: gi|148935524|gb|EC879565.2|EC879565
EST:     CCACTCCTCGCGATTGATGTTTGGGAG                         CATGCATACTATCTGGATTACGAG
genomic: CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG
EST: gi|78026637|gb|DV495024.1|DV495024
EST:     CCACTCCTCGCGATTGATGTTTGGGAG                         CATGCATACTATCTGGATTACGAG
genomic: CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG

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: 27 (upstream exon), 24 (downstream exon)
Score: 50

CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG


Block sizes: 27 (upstream exon), 27 (downstream exon)
Score: 100

CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG


Block sizes: 32 (upstream exon), 24 (downstream exon)
Score: 27

CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG


Block sizes: 27 (upstream exon), 24 (downstream exon)
Score: 15

CCACTCCTCGCGATTGATGTTTGGGAGgtatagtttt ... ccggggacagCATGCATACTATCTGGATTACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACTCCTCGCGATTGATGTTTGGGAGgtatagttttgacattgtacttttcctttcctttcgttttcataaagtttacatctttactaacaattatcttcacttccggggacag

-  CTCCTC