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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAATGTGGTGCTTCTAGAGATGTGGAAGAGATAAAAAATATGAGAAGCGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgtctaaagattaaatgtctctgaaaaaaactctgacatctggtcaaaatgatcatcgagtccatttgttgtacctaatacatatattaccttaatgagggaaatag

Basic information

species Zea mays
transcript GRMZM2G457881_T01
intron # 12
splice site 5'
intron type U12 (go to U12 genes for details)

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|211477964|gb|FL457116.1|FL457116
EST:     TATCGGATAAAGCATCTTCATTTCTTTCATCAGGAA                         ATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAATTAGAGAGAA
genomic: TATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAA
EST: gi|149023563|gb|EE154541.2|EE154541
EST:     CGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAA                         ATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAA
genomic: CGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAA
EST: gi|71322958|gb|DR798156.1|DR798156
EST:     CGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAA                         ATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAA
genomic: CGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAA

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: 48 (upstream exon), 46 (downstream exon)
Score: 92

CAAAAATGTGGTGCTTCTAGAGATGTGGAAGAGATAAAAAATATGAGAAGCGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAAATCTGTACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACT


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 22

CAAAAATGTGGTGCTTCTAGAGATGTGGAAGAGATAAAAAATATGAGAAGCGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAAATCTGTACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 66

CAAAAATGTGGTGCTTCTAGAGATGTGGAAGAGATAAAAAATATGAGAAGCGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAAATCTGTACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 18

CAAAAATGTGGTGCTTCTAGAGATGTGGAAGAGATAAAAAATATGAGAAGCGAAATACTACAGTTATCGGATAAAGCATCTTCATTTCTTTCATCAGGAAgtatccttgt ... agggaaatagATAAGGCTGAAGCAGGTTCTATCTACAAGATAATCGAACAGTTAGAGAGAAATCTGTACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACT