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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactgattaatcatttttcagttccttgaggatgtgccaataacttgccatcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 10
------------------------------------gtaaggactgattaa-tcatttttcagttccttgaggatgtgccaataacttgccatcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA
                                     ||  |    ||||| ||| | ||   ||   | |  |      | |||||  |  | ||| |||||||| |||||||| |||||||||||||| || ||||||||||||||||| ||||||||||| || || || ||||||||||| |||||||||||||| 
gtaaggaataggcaatcagtttcatcatctctctttttattgctccattaactcaatatttcattatctaaaaa------attaactcactgttttgtagGTATGTTGAGAAAACTGGACACAGAGCAGTGTACACAACTGGAAAAGGAGCTTCTGCTGTTGGACTCACCGCAGCAGTTCACAAGGATCCAGTAACACGG

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 9
--------------gtaaggactgattaatcatttt---tcagttccttgaggatgtgccaataacttgccatcttgc----agGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA
               |      |  || ||   |||     |||   |     ||   | ||  | ||   ||  |||    |||||||| || ||||| ||||| ||||| ||||| || ||||| ||||| || ||||| || ||||||||||| || ||||| || |||||||| ||| | 
gtagaattttctcaattttattttgttgatatctttatactagtgattaataaattaacaaaatatttcaaattctgctgcaagGTATGTTGAAAAAACTGGACAGAGAGCTGTATACACTACTGGTAAAGGGGCTTCTGCCGTGGGTCTTACTGCCGCGGTTCATAAGGATCCAGTCACAAGG

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagga-------ctgattaa-tcattt--ttcagttccttga-ggatgtgccaataacttgc-------catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA
||||| |       ||||  |  | | ||  || |  || |||  | || |    || |  |||         ||||  |||||||| || ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| || || ||||| |||||||||||||| ||| | 
gtaagaaaactatcctgaccagcttacttaattaatatctttggtgaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG

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|211351173|gb|FL066633.1|FL066633
EST:     AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTCAA                         GTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC
genomic: AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC
EST: gi|29544563|gb|CB604943.1|CB604943
EST:     AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAA                         GTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC
genomic: AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC
EST: gi|29544433|gb|CB604813.1|CB604813
EST:     AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAA                         GTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC
genomic: AATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGC

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: 432

GTGGACAAGAGAAGAATGTGAAGGGAAAACATCGCCTGAGAGGCGACATCAATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 93

GTGGACAAGAGAAGAATGTGAAGGGAAAACATCGCCTGAGAGGCGACATCAATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 52

GTGGACAAGAGAAGAATGTGAAGGGAAAACATCGCCTGAGAGGCGACATCAATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 34

GTGGACAAGAGAAGAATGTGAAGGGAAAACATCGCCTGAGAGGCGACATCAATGTCCTCCTCCTGGGTGATCCAGGCACTGCAAAATCACAGTTTCTTAAgtaaggactg ... catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaatcatttttcagttccttgaggatgtgccaataacttgccatcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA
                                  caataac  putative branch site (score: 34)
                                            ccatctt  putative PPT
     aatcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggactgattaatcatttttcagttccttgaggatgtgccaataacttgccatcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG