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

CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagtttatcttgctatgttattcttgttatgttgtttatattactccctgagctatattaatgttgaagtactggaatatcattctgccaacag

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 5'ss of exon 2
CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagtttatcttgctatgttattcttgttatgttgtttatattactccctgagctatattaatgttgaagtactggaatatcattctgccaacag
||| ||||| ||||||||||| || ||||||||||||||||| |||||||||||| | |||||||| ||||||||||| |||||||||||||||||||||||||| || ||  |||   | | |     || || |   |||  | ||  |   | |||||| | |||  |||| | |||| ||  || ||   |   ||
CCGCCAGACCCAGGTCATGGGCGTCATGAAGCAGGAGCAGCCCGAGCGGTACCTCAGGCTTGAGCATCTCCTTGTCCGGACATACTTTGACCCCAATGAGgttggtaacttgctctccatgtatatagttttttgtagcgttctttttcttgttttagctatctaaattgtgaatttctggtatgccactccatcgctag
















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|211187504|gb|FL065077.1|FL065077
EST:     ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCCATGAG                         GCCTACCAAGAATCCACCAGGGAGAAGCGG
genomic: ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGG
EST: gi|60351616|gb|DN218589.1|DN218589
EST:     ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAG                         GCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
genomic: ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
EST: gi|76010783|gb|DT937953.1|DT937953
EST:     ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAG                         GCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
genomic: ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
EST: gi|211187508|gb|FL065081.1|FL065081
EST:     ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAG                         GCCTACCAAGGATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
genomic: ACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     GCACCTCCTTGTCCGCACATACTTTGACCCCAATGAG                         GCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG
genomic: GCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG

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: 158

CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG


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

CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 34

CCGTCAGACGCAGGTCATGGGTGTTATGAAGCAGGAGCAGCCTGAGCGGTACCTCCGCCTTGAGCACCTCCTTGTCCGCACATACTTTGACCCCAATGAGgttggcaagt ... ctgccaacagGCCTACCAAGAATCCACCAAGGAGAAGCGGCGAGCACTGATTGCTCAAG