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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcag

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 5'ss of exon 6
GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcag
||||| ||||| || || ||||| || ||||| || |||||||||||||| || ||||||||||| |||||||  ||| ||  ||| ||  | ||||      | |  ||   |  ||   ||  || |     | || ||  |||| || ||   |||
GAAGTTCGGAGGCGAGGCCTCAAATGTTCTGTGGTTGGTGTCCCAAAGACCATAGATAACGACATTGCGgtactttcttctt-tccagcacacttgagtttggattttct---tcatgctaatcgctaa-----gattgatgttgaattgtttgcacag
















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|116813643|gb|EC856113.1|EC856113
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|33099629|gb|CF059589.1|CF059589
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     TCAAGTGCTCTGGTGTCCGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCCTTTGGATTTGACACT
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACT
EST: gi|87153260|gb|DY398049.1|DY398049
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|211450005|gb|FL281917.1|FL281917
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|211450006|gb|FL281918.1|FL281918
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG

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), 47 (downstream exon)
Score: 27

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 226

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 53

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG