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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttcattagctgatcgtgatggtgtgctgttgattcttgctctgggtgctgattctttacctgtgggtttaatcttattactgttttttttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 1
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|211511212|gb|FL158325.1|FL158325
EST:     ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGAC                         CTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
genomic: ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
EST: gi|211511214|gb|FL158327.1|FL158327
EST:     ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGAC                         CTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAGATTA
genomic: ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAGATTA
EST: gi|211511210|gb|FL158323.1|FL158323
EST:     ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGAC                         CTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
genomic: ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
EST: gi|211188745|gb|FL459412.1|FL459412
EST:     ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGAC                         CTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
genomic: ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
EST: gi|211511213|gb|FL158326.1|FL158326
EST:     ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGAC                         CTTAATATAGATNAGAGCCCGTTTCAACGGACATATGCTGCCCAG
genomic: ACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG

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: 49 (upstream exon), 45 (downstream exon)
Score: 195

ATCGGAGGCGATGCAGCTGGTGCAGGTCATCATACCCGCTGAGTCAGCGCACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 372

ATCGGAGGCGATGCAGCTGGTGCAGGTCATCATACCCGCTGAGTCAGCGCACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 160

ATCGGAGGCGATGCAGCTGGTGCAGGTCATCATACCCGCTGAGTCAGCGCACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 256

ATCGGAGGCGATGCAGCTGGTGCAGGTCATCATACCCGCTGAGTCAGCGCACCTCACCGTCTCCTACCTCGGAGACCTCGGCCTCCTCCAGTTCAAAGACgtatggttgc ... tttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtgctgattctttacctgtgggtttaatcttattactgttttttttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG
                                  ttactgtttttttt  CT-rich tract
                        tttaatcttattactg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttcattagctgatcgtgatggtgtgctgttgattcttgctctgggtgctgattctttacctgtgggtttaatcttattactgttttttttgccacagCTTAATATAGATAAGAGCCCGTTTCAACGGACATATGCTGCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
tgcttca
- - - - - gctgatc
- - - - - - - - - -gatggtg
- - - - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - ggtgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt