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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgtacagtggcaggagttattcaatcaccatctgcatttaggaagtaagttcacagcgatcgatggcactaattatcttgtcaatatatgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG

Basic information

species Zea mays
transcript GRMZM2G132804_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 10
-tggtgtacagtggcaggagttattcaatcaccatctgcatttaggaagtaagttcacagcgatcgatggcactaattatcttgtcaatatat-gcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG
 || ||| |        |   || |   |    |  |    ||  | |   |||  |||     |  || ||   ||| |  ||||||| | | |||| ||||| || |||||||| || |||||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| ||||
atgctgttcctcacggaggtctagttttttgtgaaatttgctttcgtac--agtgtacaagatgccttgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 10
tggtgtacagtggcaggagttattcaatcaccatctgcatttaggaagtaagttcacagcgatcgatggcactaattatcttgtcaatatatgcatt-tagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG
                                               ||  |||    || |    |  |       ||          | || |    |||| |||||  | ||||| |  |||||||||||||| ||||| || |||||||||||||||||  | || || |||||||| || ||  |  || | || |
-----------------------------------------------gtcggttttgtgcaaattctatccgctgccattcaactctcttgtgtaaaacagGAGCTCAACATTCCGGAAAGAGATGTGGAGCAGCTCTTGGTGTCTCTCATCCTGGACAACCGGGTTCACGGTCACATAGATCAAGTTCATCAGCTCCTGG

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 10
tggtgtacagtggcaggagttattcaatcaccatctgcatttaggaagtaagttcacagcgatcgatggcactaattatcttgtcaatatatgcatt-tagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG
                                               ||  |||    || |    |  |       ||          | || |    |||| |||||  | ||||| |  |||||||||||||| || || || |||||||||||||||||  | || || |||||||| || ||  |  || | || |
-----------------------------------------------gtcggttttgtgcaaattctatctgctgccattcaactctcttgtgtaaaacagGAGCTCAACATTCCGGAAAGAGATGTGGAGCAGCTCTTAGTGTCTCTCATCCTGGACAACCGGGTTCACGGTCACATAGATCAAGTTCATCAGCTCCTGG

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|29945495|gb|CB815668.1|CB815668
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|32935315|gb|CF040127.1|CF040127
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|32937219|gb|CF042038.1|CF042038
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|29945633|gb|CB815739.1|CB815739
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|60401353|gb|DN234160.1|DN234160
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|14202790|gb|BG836467.1|BG836467
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
EST: gi|32164838|gb|CD670156.1|CD670156
EST:     TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAG                         GAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC
genomic: TCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATC

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: 119

CCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 65

CCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

CCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 46

CCGTAACTATATTGAGGATCTGTTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAACCGTATACACGAATCAGGATTCCATTCATTTCGCAGgtagatattt ... atgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaagttcacagcgatcgatggcactaattatcttgtcaatatatgcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG
                        cactaat  putative branch site (score: 46)
                                        aatatatgcattta  TA-rich tract