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

...tctgttgtctgaaagaaaagatcaatgctgtgcaagatggagtatcgaggataattttttaagccatacatgttcctcatattgttgtgccatattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 8
tctgt-tgtctgaaagaaaagatcaatgctgtgcaagatggagtatcgaggataattttttaagccatacatgttcctcatattgttgtgccatattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG
|  || | | | |        || || |   |||  ||  |    |   |     | || | |   |  |||  |  |  | || |||||  || |||||||||||  | ||||| ||  |||||||| | | |||||||||||||||||||||  || ||||||||||| |||||||| ||||||| || || |||||||
tgggtgtatataattttttttataaaagtaatgctggaaagttctttttgttctgtcttatcatgtactcat-ctgattgtgttattgtgtaattttgcagAAACTATTACATGAAGAATCATATACAACAGAAGAAATAGAGAAAATTACAGGTCAAAGCCTGACATCTATCTTCCAGAGCTCTCAAACTTCCTTGGATG
















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|60349907|gb|DN216880.1|DN216880
EST:     GATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: GATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|67018909|gb|CO447658.1|CO447658
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|149071532|gb|EE159923.2|EE159923
EST:     GATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: GATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|76011230|gb|DT938400.1|DT938400
EST:     GATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: GATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|78111011|gb|DV529408.1|DV529408
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|32833835|gb|CD973513.1|CD973513
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|148960155|gb|EE153405.2|EE153405
EST:     TCCTGCAGTAGCTGTGAGG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|17921536|gb|BM259187.1|BM259187
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGGTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|211541591|gb|FL022794.1|FL022794
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGGTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|17921866|gb|BM259517.1|BM259517
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGGTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|32943061|gb|CF047880.1|CF047880
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|211541592|gb|FL022795.1|FL022795
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAAGACCCATATACAGGTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|71318358|gb|DR795941.1|DR795941
EST:     TCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|32835728|gb|CD975406.1|CD975406
EST:     TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: TTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
EST: gi|71773515|gb|DR971415.1|DR971415
EST:     AAGGTTCATTTGATCCTGCAGTAGCTGTGAAG                         AAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA
genomic: AAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACA

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: 99

AAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

AAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

AAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

AAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGAGAGAAGGTTCATCTGATCCTGCAGTAGCTGTGAAGgtgcacgact ... catattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaggataattttttaagccatacatgttcctcatattgttgtgccatattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG
     ataattttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttgtctgaaagaaaagatcaatgctgtgcaagatggagtatcgaggataattttttaagccatacatgttcctcatattgttgtgccatattgcagAAACTTCTGCATGAGGACCCATATACAGCTGGAGAAATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
-ctgttgt
- - - - - - aagaaaa
- - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgt