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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgtcctttatgctgttcatttcatggagccttcctttttttattgtcattaaatatttgatttatttgatacag

Basic information

species Zea mays
transcript GRMZM2G155729_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155729_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 5'ss of exon 9
CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgtcctttat-------gctgttcatt-tcatggagccttcctttttttattgtcattaaatatttgatttatttgatacag---------------------
||||||||||| |||||||||| || |||||||||| || |||||| || ||||||||||||||||||||||| ||||||||||| |||||    ||| |         | |  ||| | |||| ||||  || |    ||  |  |||| |  |    || |||   | |                      
CTCTAAAATCTCAAAGGTTGCTGGACGATATGGCTGGAAGAGGTGTGAAATATGTAGATTGCTATGGAGTTGACAATGTATTGgtgagtacactttttttttaaaaaaatatatattgtaatggggcctctctctccccatc-tgtttaattgatctccttttttaccagaataatcaatctctttgatacag

upper sequence: GRMZM2G155729_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G09170.1 (Glycine max), 5'ss of exon 9
CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagt-acgtcctttatgc---tgttcatttcatggagc--cttcctttttttattgtcattaaatattt---gatttatttgatacag------------
|||| |||||||  |  ||  | || ||||||||  |||||||  |||||||| | ||||||||||||||||| |||| | |||||| | |  | |||  | |   | ||  | ||||  | |   || | |  |   || ||| |   |||||   ||  ||||   ||               
CTCTGAAATCTACCAAATTATTGGAGGATATGGCCTCAAAAGGAATTAAGTATATTGATTGCTATGGAGTTGACAATGCACTGgtaatttattttcttgcttcctatttttctctcattaatcaattttcctggtcagttatcacttcttatttaaagaaatattgattaggatttgtgaaacag
















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|74243750|gb|DT651664.1|DT651664
EST:     CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTG                         GTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA
genomic: CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA
EST: gi|211407698|gb|FL252163.1|FL252163
EST:     CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTG                         GTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA
genomic: CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA
EST: gi|211407699|gb|FL252164.1|FL252164
EST:     CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTG                         GTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA
genomic: CTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTA

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: 46 (upstream exon), 49 (downstream exon)
Score: 38

CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTATCTGCTGCTGCTAAGGTTGTCAGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTATCTGCTGCTGCTAAGGTTGTCAGGAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 46

CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTATCTGCTGCTGCTAAGGTTGTCAGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

CTCTAAAATCTAAAAGGTTGCTCGATGATATGGCTGCAAAAGGTGTTAAGTATGTAGATTGCTATGGAGTTGATAATGTATTGgtaagtacgt ... tttgatacagGTCCGTGTTGCAGATCCAACATTCCTAGGATACTTCATTGACAGAGGTGTATCTGCTGCTGCTAAGGTTGTCAGGAAG