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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttccactagcttgtaaatttgattggagacccttgtttacacaattttccagcaccccccccccacaatccatttgcctcatgttatataccttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG

Basic information

species Zea mays
transcript GRMZM5G824405_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
gttccactagcttgtaaatttgattggagacccttgtttacacaattttccagcaccccccccccacaatccatttgcctcatgttatatacc--ttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
   | ||  ||||  | | |        |    |   ||||    || |  |  |     |||||| ||    |||   |    | || | ||  || |||||||||| || || ||||||||||||||||||||||| |||||||||||||| || || |||||||||||
--actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
















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|78022287|gb|DV490674.1|DV490674
EST:     GAAAAGTAAACCTGAAGAATATGA                         ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST: gi|84980594|gb|DW530943.1|DW530943
EST:     GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA                         ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST: gi|78021450|gb|DV489837.1|DV489837
EST:     GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA                         ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST: gi|67015674|gb|CO444423.1|CO444423
EST:     GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA                         ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA                         ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAAGAGA-TCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA

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), 45 (downstream exon)
Score: 86

ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 107

ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 131

ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccagcaccccccccccacaatccatttgcctcatgttatataccttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
                                            taccttctc  CT-rich tract
                                    atgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccactagcttgtaaatttgattggagacccttgtttacacaattttccagcaccccccccccacaatccatttgcctcatgttatataccttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - cactagc
- - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - tacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtta