Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctccactcacgttcttctaacctatctccttgtatttttgttctttattttcctgcggtccttctagcgcatcgatagatctagtatgtccatat...

Basic information

species Zea mays
transcript GRMZM2G007229_T01
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

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|94476551|gb|EB705509.1|EB705509
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|71771627|gb|DR969564.1|DR969564
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|149088158|gb|EE177297.2|EE177297
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|78122102|gb|DV540486.1|DV540486
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|78120030|gb|DV538414.1|DV538414
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|94475735|gb|EB704693.1|EB704693
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|94475779|gb|EB704737.1|EB704737
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
EST: gi|31353753|gb|CD438110.1|CD438110
EST:     CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAG                         GAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA
genomic: CTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACA

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), 48 (downstream exon)
Score: 116

AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACACCATGCTAAAAGAATGTGGAATGAGTCCCCAAAATATGATCCTGATTCA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 126

AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACACCATGCTAAAAGAATGTGGAATGAGTCCCCAAAATATGATCCTGATTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 110

AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACACCATGCTAAAAGAATGTGGAATGAGTCCCCAAAATATGATCCTGATTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 89

AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctcca ... gcttgatcagGAACATCTTTCATCTATTAACTCAACGAGAGGTCTCACCTCGATTGAAACACCATGCTAAAAGAATGTGGAATGAGTCCCCAAAATATGATCCTGATTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTAGGGCCGCGAGAACGCATCGACGGGAGGGCGAGCGAAACCACGTCCTCGATGCGCGAATCCTGGAGCCTCAGCGACAGAGATCGAATCCAATCAGgtatcctccactcacgttcttctaacctatctccttgtatttttgttctttattttcctgcggtccttctagcgcatcgatagatctagtatgtccatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC