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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctctatcttatactggagtattaatttttctgcttctaagcatgttttccagctggcatacgagtgtgcttgctaagcattattatgattcatt...

Basic information

species Zea mays
transcript GRMZM2G330650_T02
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|21810005|gb|BQ668323.1|BQ668323
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|87157738|gb|DY402527.1|DY402527
EST:     ACAAACTGTTGAGACTGGAGCTCAAACTTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: ACAAACTGTTGAGACTGGAGCTCAAAC-TGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|60338704|gb|DN205677.1|DN205677
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|110510919|gb|EE019261.1|EE019261
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|7135591|gb|AW498164.1|AW498164
EST:     AAACTGTTGAGACTGGAGCTCAAACTGCTGCGCCATTAACNCAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: AAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|18166041|gb|BM335880.1|BM335880
EST:     AGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: AGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|149097830|gb|EE183757.2|EE183757
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|50334133|gb|CO529259.1|CO529259
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|89754547|gb|DY685289.1|DY685289
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGGGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCC
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|76286033|gb|DV025601.1|DV025601
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
EST: gi|76913444|gb|DV165140.1|DV165140
EST:     CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAA                         ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA
genomic: CACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCA

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: 38 (upstream exon), 48 (downstream exon)
Score: 74

TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 94

TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 158

TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 123

TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctct ... ttttttgtagACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCCTGTTTGCCATGGCAAAATTTACAAGACATTCTTGTAGGTCGTAGCACAAACTGTTGAGACTGGAGCTCAAACTGCTGCGACATTAACACAGCAAgtatgcctctatcttatactggagtattaatttttctgcttctaagcatgttttccagctggcatacgagtgtgcttgctaagcattattatgattcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC