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

ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattttttgttctatatgttagcatattgtgtttgtgtataatgggccttggcccatgtcttgactatatgttaatatattccctgaccattagg...

Basic information

species Zea mays
transcript GRMZM2G078576_T04
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattttttgttctatatgttagcatattgtgtttgtgt-ataatgggccttggcccatgtcttgactatatgttaatatattccctgaccattagg--
|||||||| ||||| ||||||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| ||||| |||||||  |||  |||||| | | |  || | |  ||| |     | |||| |  |      |    |||    || ||  ||  |      ||  | ||    
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctct-taggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggt--atgcagcgagcgatgactaaaaa
















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|37377989|gb|CF625644.1|CF625644
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|71438781|gb|DR819831.1|DR819831
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|149083574|gb|EE172908.2|EE172908
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTTTCCTTCAATCCCAGCGCCATAAATTTTTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|87155515|gb|DY400304.1|DY400304
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAACGCCATAAATCTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|78111274|gb|DV529671.1|DV529671
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAGCGCCATAAATCTTTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|71759659|gb|DR957596.1|DR957596
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTTTCCTTCAATCCCAGCGCCATAAATCTTTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|22472877|gb|BU037357.1|BU037357
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAACGCCATAAATCTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|24766669|gb|CA401816.1|CA401816
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCCCCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|37376751|gb|CF624930.1|CF624930
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|148945634|gb|EC890893.2|EC890893
EST:     CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTTTCCTTCAATCCCAGCGCCATAAATTTCTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT
EST: gi|93282383|gb|EB674647.1|EB674647
EST:     CCTGAGGAATTCTTTTTCCCATATGCATGGCGCCTTGTCCTGTCACGGGG                         ATTTTCCTTCAATCCCAGCCCCATAAATTTTTTCCCTGTGGAGATTCACCT
genomic: CCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCT

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), 48 (downstream exon)
Score: 47

ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA


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

ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattt ... caattcacagATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA