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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggcagtgaaataataattaagtaattattacttgtattacttgcaaactccatactgtgtgaaggatgacatatttctagatgcttggttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG

Basic information

species Zea mays
transcript GRMZM2G011575_T01
intron # 11
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|24765764|gb|CA400923.1|CA400923
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|148930025|gb|EE285908.2|EE285908
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|211108201|gb|FL028207.1|FL028207
EST:     CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAATATG                         TGCAAGATCTCTTCGTGGARGTGCAAGCATTTTGCATCGCCTTCTCGCGA
genomic: CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAG-ATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
EST: gi|89251017|gb|DY622803.1|DY622803
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|211108200|gb|FL028206.1|FL028206
EST:     CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAATATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
genomic: CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAG-ATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
EST: gi|113701502|gb|EE679006.1|EE679006
EST:     ATTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|40303841|gb|CK348228.1|CK348228
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|71769411|gb|DR967348.1|DR967348
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|91049014|gb|EB159432.1|EB159432
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|74239167|gb|DT647081.1|DT647081
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA

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), 49 (downstream exon)
Score: 63

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 28

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaactccatactgtgtgaaggatgacatatttctagatgcttggttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG
                           atatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggcagtgaaataataattaagtaattattacttgtattacttgcaaactccatactgtgtgaaggatgacatatttctagatgcttggttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG

- - - - - - - - - - - - - - -ttacttg
- - - - - - - - - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg