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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTCCATCCTCGAATCTTTGAGGAGGAGAGCGCGCATGATGACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatcaagatttctgttggtttgcagcgaatagagtgtggtttatttttgtgactggttgtgttgctgcag

Basic information

species Zea mays
transcript GRMZM5G840582_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 10
CAAGTCCATCCTCGAATCTTTGAGGAGGAGAGCGCGCATGATGACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatcaagattt----ctgttggtttgcagc----gaatagagtgtggt--ttatttttgtga-------ctggttgtgttgctgcag
|||||| |||||||| ||||||||||||||||| ||| |||||||||| |||||||| || |||||||| || || |||||||||||||||||| | ||| || || |    |  ||  |||   ||    | | | | ||  |    |  | |  | |       |   || ||||| |||||
CAAGTCTATCCTCGAGTCTTTGAGGAGGAGAGCACGCCTGATGACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtga-cattaacatatgagccccttcctttatggcaataggagaaaatgaagcagcttctctaataatgctcttccaattatgttgttgcag

upper sequence: GRMZM5G840582_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G23310.2 (Arabidopsis thaliana), 5'ss of exon 12
CAAGTCCATCCTCGAATCTTTGAGGAGGAGAGCGCGCATGATGACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaag-catcaagatttctgttgg----tttgcagcgaatagagtgtgg-----tttatttttgtgactggttgtgttgctgcag-------------
||||   || || ||||||||||| || |||||  |  | |||||||| || ||||||||||||  |||||| |||||||||||||||||||||||  ||  ||     |  || |    | ||||| | | | | | |||     | | || |||    || |  | |   |   |             
CAAGGGGATTCTTGAATCTTTGAGAAGAAGAGCAAGGCTCATGACAGATGGATTCAACAGCTGCAAAAACGTCGTGTGCAATTTCACAGAAGgtaaaacaataatgaagcaattagcacctgtgcagtgtagaaaatttgggagtatatgttgttgaagttgatcctttaattcttggtgtaaatgttag
















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|78112475|gb|DV530869.1|DV530869
EST:     GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     GACAGACGGTTTCAACAGCTGCCGAAATGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
EST: gi|7238269|gb|AW573536.1|AW573536
EST:     GACAGACGGTTTCAACAGCTGCCGAAATGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCNCCAAATACAGCTGCCAGCAAGAGCCATCGAG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCC-CCAAATACAGCTGCCAGCAAGAGCCATCGAG
EST: gi|110203147|gb|EC885044.1|EC885044
EST:     GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
EST: gi|91054117|gb|EB164535.1|EB164535
EST:     GACAGACGGTTTCAACAGCTGCCGAAATGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTTTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
EST: gi|5917498|gb|AW054301.1|AW054301
EST:     GTTTCAACAGCTGCCGAAATGTGGTGTGCAATTTCCCAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
EST: gi|7227753|gb|AW566394.1|AW566394
EST:     GACAGACGGTTTCAACAGCTGCCGAAATGTGGTGTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG
genomic: GACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGG

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

CAAGTCCATCCTCGAATCTTTGAGGAGGAGAGCGCGCATGATGACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatca ... gttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGGCGGCAAAGAGAGCCGGCAAAGCAGCAGACGTTTTCTACTGCCTCAAGCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGTCCATCCTCGAATCTTTGAGGAGGAGAGCGCGCATGATGACAGACGGTTTCAACAGCTGCCGAAACGTGGTGTGCAATTTCACAGAAGgtaagcatcaagatttctgttggtttgcagcgaatagagtgtggtttatttttgtgactggttgtgttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC