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

gtaataagtgtgtgtgtatttgcttcagttctatacacgaagtaattcatcgttgggctgtgatggacaatttttcttttacttgtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG

Basic information

species Zea mays
transcript GRMZM5G824600_T02
intron # 3
splice site 3'
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|148969452|gb|EE020260.2|EE020260
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|149055770|gb|EE156478.2|EE156478
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|148972824|gb|EE023810.2|EE023810
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|32944033|gb|CF048852.1|CF048852
EST:     GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|149107259|gb|EE189142.2|EE189142
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|149001497|gb|EE038802.2|EE038802
EST:     GATCCTGAGGGTC-TTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|148930859|gb|EC873272.2|EC873272
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|211403715|gb|FL311339.1|FL311339
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|84980410|gb|DW530759.1|DW530759
EST:     GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|148971977|gb|EE022778.2|EE022778
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|31355494|gb|CD439851.1|CD439851
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|31355865|gb|CD440222.1|CD440222
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|211233989|gb|FL398757.1|FL398757
EST:     GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCTGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|149103654|gb|EE289058.2|EE289058
EST:     GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGG                         AATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
EST: gi|20811111|gb|BQ295589.1|BQ295589
EST:     GATCCTGAGGGTCTTTTTCCTTGCATTCTTGGCCACGAAGCTGCTGG                         AATTGTTTTAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA
genomic: GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 692

GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 957

GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 456

GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 498

GATCCTGAGGGTCTTTTCCCTTGCATTCTTGGCCACGAAGCTGCCGGgtaataagtg ... gtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaattcatcgttgggctgtgatggacaatttttcttttacttgtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG
                               tttttcttttacttgt  CT-rich tract
                             aatttttcttttactt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataagtgtgtgtgtatttgcttcagttctatacacgaagtaattcatcgttgggctgtgatggacaatttttcttttacttgtcttaatagAATTGTGGAAAGTGTCGGTGAAGGAGTAACTGATGTGCAGCCTGGGGATCATGTCATTCCTTGCTACCAAGCAGAATGCAAAGAATGCAAGTTTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA