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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgcactggaggcttcctattagaatgatgtctgctttgtaagcacaaatgaattgtaaactgacctgtcaatattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG

Basic information

species Zea mays
transcript GRMZM2G028307_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028307_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g33420.1 (Oryza sativa), 3'ss of exon 9
gtacc-tgcactggaggcttcctattagaatgatgtctgctttgtaagcacaaatgaattgtaaactgacctgtcaatattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGA---ACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG
||||| || | |  |  | | ||  ||||           |||||| ||  ||||  |     ||    | |||  | |||| ||||||||| ||||||||||||||||||| || || | |||    |||||| |||  || |  ||     ||| ||| |  ||  | |||| ||||||  |||   
gtaccctgtattttattcgtactgatagagca-------ttttgtaggcgtaaatacaacactaa---gcttgtacaaatttccagTTCCATCATGTGCACAGTGAAAGGACTTCCAAAGAAGACAAGCATTCTAGTCGTTTCATATCCGAAGATCTTGTACACGTACCAAAGATTGATGGTGTAT---
















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|32932602|gb|CF037414.1|CF037414
EST:     CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAG                         TTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC
genomic: CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC
EST: gi|32940378|gb|CF045197.1|CF045197
EST:     CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAG                         TTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC
genomic: CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC
EST: gi|32945347|gb|CF050166.1|CF050166
EST:     CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAG                         TTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC
genomic: CCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCAC

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), 49 (downstream exon)
Score: 145

GTATGGAGGAGATTTGAGGAATCTTGACGATAGTACATTAAACATAATTACCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG


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

GTATGGAGGAGATTTGAGGAATCTTGACGATAGTACATTAAACATAATTACCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 37

GTATGGAGGAGATTTGAGGAATCTTGACGATAGTACATTAAACATAATTACCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GTATGGAGGAGATTTGAGGAATCTTGACGATAGTACATTAAACATAATTACCAATTCTGGTTTGTTGAAGATAAACCACTATAGTAGAAATAACATGGAGgtacctgcac ... atattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtctgctttgtaagcacaaatgaattgtaaactgacctgtcaatattttcagTTCCATTATGTGCACAGTGAAAGGACATCAAATGGAGAACATTCTGGTCACTTTAGGTCTCCTTATCCTGTTCGTGTTACCAAGAATGATGGCATATTTG
                                aactgac  putative branch site (score: 164)
                                              tattttc  putative PPT
                    aaatgaattgtaaa  TA-rich tract