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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaaagacaaaaaaatcacccataagatttatatgggttgtgctaatatatggctctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA

Basic information

species Zea mays
transcript GRMZM2G061099_T01
intron # 7
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|60336647|gb|DN203620.1|DN203620
EST:     GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAG                         GTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
genomic: GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
EST: gi|61118309|gb|DN559270.1|DN559270
EST:     GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAG                         GTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
genomic: GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
EST: gi|61118310|gb|DN559271.1|DN559271
EST:     GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAG                         GTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
genomic: GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
EST: gi|32910642|gb|CF015454.1|CF015454
EST:     GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAG                         GTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG
genomic: GCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACG

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), 48 (downstream exon)
Score: 121

TTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 88

TTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

TTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 114

TTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAGCTGACTTTTAAGGAGCAGTCTTTCCTTGATCGGAATCCTCGCCAGgtaaagaaag ... tctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaatcacccataagatttatatgggttgtgctaatatatggctctatggaagGTTCAAGGAGTCGTCAAGGATGCTGGTGGAAGCAAGGTTGCAACATTGACGGGGAAGTGGGATGAAAGTGTGCATTGTGTCATCAACAATGATGCCTCTA
                               tgctaat  putative branch site (score: 114)
            ataagatttatat  TA-rich tract