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

GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttgatcttatgcggatgaaaaatgtaatattgttgaagtacttttctgtgcaagtttatatatctctgactattttgacatttaacag

Basic information

species Zea mays
transcript GRMZM2G033515_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033515_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 4
GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttgatcttatgcggatgaaaaatgtaatattgttgaagtacttttctgtgcaagtttatat-atctctgactattttgacatt-taacag
|||||||||||| |||||||||||||| ||||||||||||| |    || ||| | ||      | | | ||   | | ||    | |  | | ||  |   | | ||||||  ||||||  ||| | |  |||
GTACAATGTGGCTATTAAGTGTGCGACGATTACTCCAGgtaaaagatatattaagtggcctttta-tcttatgcagctaaaaagatatattcttcatttgactcttatctctttctatttcaacactattccag
















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|67021863|gb|CO450612.1|CO450612
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|31353696|gb|CD438053.1|CD438053
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|29130361|gb|CB381065.1|CB381065
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|84980627|gb|DW530976.1|DW530976
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|61119247|gb|DN560208.1|DN560208
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|78092177|gb|DV520551.1|DV520551
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|211356165|gb|FL188392.1|FL188392
EST:     GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
EST: gi|211356162|gb|FL188389.1|FL188389
EST:     TTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAG                         ATGARACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA
genomic: GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAA

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: 38 (upstream exon), 46 (downstream exon)
Score: 60

GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 78

GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 117

GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 68

GTACAATGTGGCCATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catttaacagATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG