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

...gaaaagtgcaatctacagtgcaaaactgtgttttatgtgaccatataagtgaactgctggacggtctcacattttcattgctttgtgatgacaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG

Basic information

species Zea mays
transcript GRMZM2G091563_T01
intron # 6
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|211309278|gb|FL056037.1|FL056037
EST:     TACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: TACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|30306632|gb|CD001305.1|CD001305
EST:     AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|32164812|gb|CD670451.1|CD670451
EST:     AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|60337054|gb|DN204027.1|DN204027
EST:     AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|4730783|gb|AI649949.1|AI649949
EST:     GAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCNCCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: GAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|31909603|gb|CD651001.1|CD651001
EST:     ACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: ACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|83279407|gb|DV943415.1|DV943415
EST:     CAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: CAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|32848125|gb|CD987806.1|CD987806
EST:     AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTACTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|29544108|gb|CB604488.1|CB604488
EST:     TACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCNCCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: TACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|60355748|gb|DN222721.1|DN222721
EST:     AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
EST: gi|5895629|gb|AW036875.1|AW036875
EST:     AATTGTCATACCGGGTTACGGAGGAAGATGTTATCCGTGCACGTAATCAG                         CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG
genomic: AATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAG

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: 146

GCTGATTGCTTGGATGATTTGGCTTTTGCAATTATGCATGAGATGAGCAAATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 201

GCTGATTGCTTGGATGATTTGGCTTTTGCAATTATGCATGAGATGAGCAAATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GCTGATTGCTTGGATGATTTGGCTTTTGCAATTATGCATGAGATGAGCAAATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 241

GCTGATTGCTTGGATGATTTGGCTTTTGCAATTATGCATGAGATGAGCAAATTGTCATACCGGGTTACAGAGGAAGATGTTATCCGTGCACGTAATCAGgtaatgtttg ... acaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtgaactgctggacggtctcacattttcattgctttgtgatgacaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG
                  gtctcac  putative branch site (score: 241)
                         attttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaagtgcaatctacagtgcaaaactgtgttttatgtgaccatataagtgaactgctggacggtctcacattttcattgctttgtgatgacaatttcagCTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - -cagtgca
- - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatg