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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagttgtgcctttttttgctattcttgttgtctatgaagtgtggtgtgcatggtatatatattctatccagtcacaaatatgcagtgttctgaa...

Basic information

species Zea mays
transcript GRMZM2G076484_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076484_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g20580.1 (Oryza sativa), 5'ss of exon 4
GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagttgtgccttt--ttttgctattcttgttgtctatgaagtgtggtgtgc----atggtatatatattctatccagtcacaaa--tatgcagtgttctgaa
||||| |||||||| || ||||||||||||||||||||||||||||||||| ||||  |||||||||| ||||| |||||||||||  |  | ||| |||  || || | || |   ||  | |||| |    |   |    ||||       ||  |  || | ||| ||  |||| | |        
GATATTGTCATAGGGACACCTGGTCGTATGAAAGACCTTATTGAAATGGGTATTTGTCGTCTTAATGATGTTTCTTTTGTGgtaagttaactatgcatttcattgtgttgttgtctatggttttgaattagtatacacccatatgggggcaccatggtgcccgggcaccaaggtatgtaat--------

upper sequence: GRMZM2G076484_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0109g00380.t01 (Vitis vinifera), 5'ss of exon 6
GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagttgtgcctttttttgctattcttgttgtctatgaa---gtgtggtgt-gcatggtatatatattctatccagtcacaaatatgcagtgttctgaa
|| || |||||||| |||||||| ||| |||| || || |||||||||||||| || || ||||  ||||| || |||||||||||       |   ||   |     |  ||| |   |||      || |  ||| || |   |||   |     |  | ||  ||||  |||||| ||    
GACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTGgtaagtagaggatcatttgaatcaacctatttgctaattattttcttgtattatgttgctttcaatagtcaacacgttgactctgaaattagcagtgctc----
















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|74244222|gb|DT652136.1|DT652136
EST:     AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTG                         -----A--TGAAGCAGATAGGATGCTGGATTTGGG
genomic: AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGG
EST: gi|71428435|gb|DR809485.1|DR809485
EST:     AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTG                         GTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAAACCTGA-GT
genomic: AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAA-CCTGAAGT
EST: gi|149059470|gb|EE156955.2|EE156955
EST:     AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTG                         GTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTC
genomic: AAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTC

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), 49 (downstream exon)
Score: 82

GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTCAGGGCAATTTTGAGCCAAACATCATCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTCAGGGCAATTTTGAGCCAAACATCATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTCAGGGCAATTTTGAGCCAAACATCATCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

GATATAGTCATAGGAACTCCTGGTCGTATGAAAGACCTTATTGAAATGGGTGTTTGCTGTCTTAATGAGGTTTCGTTTGTGgtaagccagt ... ttttgcatagGTTCTAGATGAAGCAGATAGGATGCTGGATTTGGGTTTTGAACCTGAAGTCAGGGCAATTTTGAGCCAAACATCATCTG