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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagctcttgacaactactatccattttgttaggctggaattaacagttcaactgacctttttcctttgcag

Basic information

species Zea mays
transcript GRMZM5G802858_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G802858_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g53760.1 (Oryza sativa), 5'ss of exon 15
AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagctctt-gacaact-----actatccattttgttaggctggaattaacagttcaactgaccttt----ttcctttgcag
|||||||||||  |||||||| || ||||||||||||||||||||||||||||| ||||| ||||||||||| ||||| || || ||| |||| ||||||||||| | || |  ||| |||     |   |||||| | || |     |   |||   |||  | |  |||    || | || |||
AGACTCTGATGCAAATACAAATAATAGTTTGAGCCATAATCAATCATTGGTCCGTGGTATCATATGTTCTGGACTTTTCCCAGGCATAACATCAGTTGTGgtaaagatctgtcagactactttgtaaagttccattctatttgaaaacacaaaacttgtcagttaatttttgagctttcctttcag

upper sequence: GRMZM5G802858_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G24630.1 (Glycine max), 5'ss of exon 19
AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaaca----gctcttgacaactactatccattttgttag-----gctggaattaacagttcaactgacctttttcctttgcag----------------------------
|||  | || |  ||    |  ||||  ||||| || ||||||||  | || || |   | |||||||||||||| |||||||| |||||||| || ||||| | |     | |  | | || |  | |   | |  | |        |    ||| |     |  ||| ||||| |  ||  |                             
AGATGCAGAAGCTAACGTCATTAACAAATTGAGTCACAATCAATCTCTTGTGCGTGCAGTCATATGTTCTGGGCTCTTTCCTGGCATAGCATCAGTGGTGgtgagctatgtgtttgttataaattttgtttttctcctcaataagtattatctttagcttacaagttgagcttttactgttttatttaattaattaattcttcctctgtacag
















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|21432114|gb|BQ547604.1|BQ547604
EST:     TCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTG                         CATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTT
genomic: TCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagct ... tcctttgcagCATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTT




















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), 44 (downstream exon)
Score: 29

AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagct ... tcctttgcagCATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTTCTTTATGCT


Block sizes: 45 (upstream exon), 30 (downstream exon)
Score: 12

AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagct ... tcctttgcagCATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTTCTTTATGCT


Block sizes: 35 (upstream exon), 41 (downstream exon)
Score: 12

AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagct ... tcctttgcagCATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTTCTTTATGCT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 25

AGACTCTGATGGGAATACAAACAACAGTTTGAGCCATAATCAATCATTGGTCCGCGGTATTATATGTTCTGGGCTTTTTCCTGGGATAGCATCTGTTGTGgtaaacagct ... tcctttgcagCATCGAGAAAGCTCCATGTCCTTTAAGACCATGGATGACGGGCAAGTTCTTCTTTATGCT