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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccttggatttgaagctatttcctgtgctggggcttgcccctccgttctcttgagtcctcactgcttgctgcatctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA

Basic information

species Zea mays
transcript GRMZM2G375116_T01
intron # 1
splice site 3'
intron type U2

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|148943865|gb|EC888945.2|EC888945
EST:     GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
genomic: GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
EST: gi|9953376|gb|BE639959.1|BE639959
EST:     CGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
genomic: CGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
EST: gi|149000052|gb|EE037155.2|EE037155
EST:     GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
genomic: GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
EST: gi|149088206|gb|EE177323.2|EE177323
EST:     GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTAC
genomic: GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTAC
EST: gi|149080762|gb|EE169827.2|EE169827
EST:     GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
genomic: GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
EST: gi|148959440|gb|EE010791.2|EE010791
EST:     GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAG                         CGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC
genomic: GGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 102

CATGGAGCCAGCAGGCGTGGCGCATTGAGGCGTGCGTGCAGGGCCGGAGAGGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 27

CATGGAGCCAGCAGGCGTGGCGCATTGAGGCGTGCGTGCAGGGCCGGAGAGGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA


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

CATGGAGCCAGCAGGCGTGGCGCATTGAGGCGTGCGTGCAGGGCCGGAGAGGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

CATGGAGCCAGCAGGCGTGGCGCATTGAGGCGTGCGTGCAGGGCCGGAGAGGGACATGGATCTGGAGTCCGCGGACGGAGCGGAGGCGGCTGACGGGAAGgtgagtcctt ... tctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggcttgcccctccgttctcttgagtcctcactgcttgctgcatctcctgcagCGGCGTGGGGAGTCATTGCGCGCGACGCTGCTGCTCGCGTACCAGAGCCTCGGGGTGGTGTACGGCGACGTGGCCACGTCCCCGCTCTACGTCTACAAGA
                           tcctcac  putative branch site (score: 113)
                                           catctcct  putative PPT