Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcattcttgtcatatatttgccctttgaagtttttccttggaaaatttctagctgtagattattatattatagcttactttatttcccttttctccttgtctgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG

Basic information

species Zea mays
transcript GRMZM2G470292_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 2
gttggcattcttgtcatatatttgccctttgaagtttttccttggaaaatttctagctgtagattattatattatagcttactttatttcccttttctccttgtctgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG
|||||||||  | ||||||     || |||||||| |||  |  ||| |||  | | ||||| | || | |  || |  ||  | || |    ||| ||||| | | |||||||| ||||||| ||||||||||||||||||||| | |||||||| ||||| ||||| || |||||||||||||| |||
gttggcatttct-tcatat-----ccttttgaagtgtttgttcagaacattagtggttgtagctaatcaca--attgtctagctaatgtta--tttatccttctgtatgttgcagTTAATGGAATTGCTTTTCTCATTTGTGAAATCCGATCATCCACATAGCACATTGTTATCTGGTTACTTCAGCAAG
















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|211324683|gb|FL455368.1|FL455368
EST:     TTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAG                         CTAATGGATTTGCTTTTYTCATTTGTGAAACCTGATCATCCGCATAGTACA
genomic: TTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAGgttggcattc ... tgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACA




















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: 47 (upstream exon), 48 (downstream exon)
Score: 170

GTTCCCATTTATTGCTTCTGAAATATTTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAGgttggcattc ... tgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG


Block sizes: 40 (upstream exon), 45 (downstream exon)
Score: 50

GTTCCCATTTATTGCTTCTGAAATATTTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAGgttggcattc ... tgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GTTCCCATTTATTGCTTCTGAAATATTTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAGgttggcattc ... tgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 89

GTTCCCATTTATTGCTTCTGAAATATTTACTTGCGAAATCGATGTCATTTTGAGGACCCTAGTAGAGGATGAAGAGgttggcattc ... tgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattattatattatagcttactttatttcccttttctccttgtctgtgttgcagCTAATGGATTTGCTTTTCTCATTTGTGAAACCTGATCATCCGCATAGTACATTATTGTCTGGTTACTTCAGTAAG
               agcttac  putative branch site (score: 89)
                 cttactttatttccct  CT-rich tract
     attatattatagctta  TA-rich tract