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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctcacacttcattcagacttgtaacttgatacaaaatcactatcctatgttgagttaacaaggattttatactcttcaatag

Basic information

species Zea mays
transcript GRMZM5G813363_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813363_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g10740.1 (Oryza sativa), 5'ss of exon 5
TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctcacacttcattcagacttgtaacttgatacaaaatcactatcctatgttgagttaacaaggattttatactcttcaatag------
 |||||||||||||||||||| ||||| || |||||||| ||||| |||||||| ||||| ||  ||        ||| |  | | |   || |    | ||||||    || ||   || | |||  |  || ||    |  ||||| |      
ATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCAgtgagtg-------ttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcag
















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|91872830|gb|EB402787.1|EB402787
EST:     TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG                         ACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
genomic: TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
EST: gi|101391594|gb|EB817733.1|EB817733
EST:     TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG                         ACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGGTTCCCCTCTGTGC
genomic: TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
EST: gi|101387839|gb|EB815934.1|EB815934
EST:     TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG                         ACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
genomic: TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
EST: gi|71322272|gb|DR797821.1|DR797821
EST:     TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG                         ACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
genomic: TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
EST: gi|88749046|gb|DY533187.1|DY533187
EST:     TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG                         ACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC
genomic: TGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGC

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: 40 (upstream exon), 49 (downstream exon)
Score: 10

TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 22

TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 72

TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCGgtatgttctc ... tcttcaatagACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA