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

CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcagaacttttaccatgaagatacttatctgttctgttttttatgattcagtgaccgtttccatggtgtgcattcctcatttactgttttgcta...

Basic information

species Zea mays
transcript GRMZM2G036034_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 12
CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcagaact---------------tttaccatgaagatact-----tatctgttctgtttttta--tgattcagtgaccgtttc--catggtgtgcattcct-----catttactgttttgcta-------
||||| || ||||| || ||||||||||||||||||||||||||||| ||||| ||   | |  |               ||   |||||| |   |     | || |||||||| || |   |   ||   | |  | |  | |||   | |  | |     ||||| || |  |  |        
CCTCGAATTTTTGTCCTTCTGAGACGCTGCCTGTTTGATGGTGATGATGAGgtgagcaaaaagataattatgctctgttcttcctcatgaacagcttagcattgtcagttctgttcttaaaagggcccatcaaactctccttcctggcaagaagcctttcttacatttgctatgcttttcacctcag
















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|211006550|gb|FL418097.1|FL418097
EST:     CTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAG                         GTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACA
genomic: CTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACA
EST: gi|211376755|gb|FL398876.1|FL398876
EST:     TCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGAACGAG                         GTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTAC
genomic: TCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATG-ACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 193

CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACAGTTGGTGAGACAGAGAAGGATGTGAATGAATTTCTCTTCGGCTCACTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 213

CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACAGTTGGTGAGACAGAGAAGGATGTGAATGAATTTCTCTTCGGCTCACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACAGTTGGTGAGACAGAGAAGGATGTGAATGAATTTCTCTTCGGCTCACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

CCTCGCATATTTGTGCTCCTGAGACGCTGCCTGTTTGATGGTGATGACGAGgttagtgcag ... tatcttgtagGTGCGCGACAGAGCAACCCTTTACCTCAAATTGTTAGGTGGGGAAGCTACAGTTGGTGAGACAGAGAAGGATGTGAATGAATTTCTCTTCGGCTCACTTG