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

...ctgttacatttgaccctttcctactatcatgcaatcttaagtgcctattgcggacaggactttgtgtacattataattgaagcgttttttcttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG

Basic information

species Zea mays
transcript GRMZM2G118316_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 12
-ctgttacat--ttgaccctttcctactat-catgcaatcttaagtgcctattgcgga--caggactttgtgtacattataattgaagcgttttttcttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG
  |||  | |  || |    |||    ||| | |  |   |  ||||   || || |     | | |||| ||     |||| || | | | |||||  |||| |  || || |||||||  |||||||||||||| |||||||||||||||||||| || ||||| |||||||| || |||||||||||||||
tttgtctccttattcaaatattcaagttattcgtttatattggagtgtgcatggcagtacttgcattttgggtgtgacataaatggaacatcttttc--cagGCATCGATGACAATGACACTATGAAGGTTTTTGGCAAGGGTGGTGCAGATGTTGAGCGCAATAAACCTGGTGATCTCTATGTTACTATCAAG

upper sequence: GRMZM2G118316_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G42640.1 (Glycine max), 3'ss of exon 12
-----ctgttacatttgaccctttcctactatcatgcaatcttaagtgcctattgcggacaggactttgtgtacattataattgaa-gcgttttttctt-caggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG
      | || |  ||||    ||  |  | | || ||||  |  | |   |      | |     |||  |   | | | ||  | |  | |    || |||| | |||| | ||||| |  || ||||||| | | |  ||||||||||||  |||  || |||| |||||||| ||||||||||||||||||
tgactatctttctattgataaatt--tgatttaat-caattatgggagaaaaaaatacaaatagggttgactgattcacatttacatgtatgtacatttgcagGGATTGACAACAATGAAACTATAAAGGTTTATAGAAGTGGTGGTGCAGATCCTGATGGAGATAATCCTGGTGATCTTTATGTTACTATCAAG
















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|71769071|gb|DR967008.1|DR967008
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGA
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGA
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     AAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|18165643|gb|BM335482.1|BM335482
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGA
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGA
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         G
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaag-
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         G
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaag-
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         G
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaag-
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         G
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaag-
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         G
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaag-
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGGAAG                      
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC----AGgtaaggagga ... cttcagg

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: 48 (upstream exon), 49 (downstream exon)
Score: 7

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... cttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcggacaggactttgtgtacattataattgaagcgttttttcttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG
                                     cgttttttcttc  CT-rich tract
                     tacattataattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttacatttgaccctttcctactatcatgcaatcttaagtgcctattgcggacaggactttgtgtacattataattgaagcgttttttcttcaggaagTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
ctgttac
- - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - ctattgc