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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaggatcctgccggcaccgtcacattcgattccccttgtattacataaacgttgttgtctgtgtgaccaattcgatctgatcccgctagctgacacctaacatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCAACATCATGAAGGATTTCGATGAGCGGGGGCACCGTACCTTGCCTCGACC

Basic information

species Zea mays
transcript GRMZM5G807327_T01
intron # 1
splice site 3'
intron type U2

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|87154786|gb|DY399575.1|DY399575
EST:     CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACG                         GGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
genomic: CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACGgtagaggatc ... acatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
EST: gi|22545102|gb|BU097461.1|BU097461
EST:     CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACG                         GGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
genomic: CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACGgtagaggatc ... acatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
EST: gi|26455623|gb|CA827206.1|CA827206
EST:     CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACG                         GGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
genomic: CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACGgtagaggatc ... acatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
EST: gi|87154165|gb|DY398954.1|DY398954
EST:     CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACG                         GGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA
genomic: CTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACGgtagaggatc ... acatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCA

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 1 RNA-Seqlibrary.


Block sizes: 23 (upstream exon), 37 (downstream exon)
Score: 6

CATTCCTCTGCCGTAAAGTCCGACGGCAGCCACGTGGTACCAGGCCACAGCTGGCCCACACGTCATCCACCCGGCTACCACAACGTTCACGGATGTTACGgtagaggatc ... acatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCAACATCATGAAGGATTTCGATGAGCGGGGGCACCGTACCTTGCCTCGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctgtgtgaccaattcgatctgatcccgctagctgacacctaacatgtgaagGGATAGATTTTGCTGTGACGTCATCCACCCAATTCAAGCCTGAGATGGCCAACATCATGAAGGATTTCGATGAGCGGGGGCACCGTACCTTGCCTCGACC
                                        acctaac  putative branch site (score: 6)