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

...atatatttgcaagtcttctggcgtgtttcccttccgtgatatatgttgaagatcacgacagatgcatggcgctaagcttatgacttttattttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC

Basic information

species Zea mays
transcript GRMZM2G152686_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 8
atatatt-tgcaagt-cttctggcgtgtttcccttccgtgatatatgttgaagat-cacgacagatgcatggcgctaagcttatgacttttattttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC
|  |||  ||||  |  |||||  |  | | | | |    || | ||||    || ||    |||   |    || ||||||||| |||    ||   | ||| ||||| ||||||||||||||||||||||| ||||||||||||||||| || || |||||  |||||||||||||||| ||  ||||||||||||  |||
aagtatggtgcacttgtttctgtagcatatgcttgcaaatat-tctgttatgtattcaacttagagatacattgccaagcttatggctt--gattcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGAAGCCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTC
















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|108954033|gb|EC364981.1|EC364981
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAA                         ATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
EST: gi|213173762|gb|FM184221.1|FM184221
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCCGGAGAAACTGCACATGGGAA                         ATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
EST: gi|6020916|gb|AW065844.1|AW065844
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAA                         ATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
EST: gi|14204276|gb|BG837953.1|BG837953
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAA                         ATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
EST: gi|211384112|gb|FL133262.1|FL133262
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAA                         ATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGA

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: 179

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 159

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcaca ... tttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagatcacgacagatgcatggcgctaagcttatgacttttattttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC
                                      cttttatttt  CT-rich tract
                                ttatgacttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatatttgcaagtcttctggcgtgtttcccttccgtgatatatgttgaagatcacgacagatgcatggcgctaagcttatgacttttattttgcgacagATTTCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - atttgca
- - - - - - - cttctgg
- - - - - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg