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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcatccgttctctccccttcctgctgtgcgaaactgaccaccgaaccctaagtttgtctatttgtattcggatctgatctaattagaagtttatatgtatacctaataaattcgatttttcctgttctttttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG

Basic information

species Zea mays
transcript GRMZM2G085427_T02
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|78119579|gb|DV537963.1|DV537963
EST:     CCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCAT                         TTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGA
genomic: CCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGA
EST: gi|211048831|gb|FL187591.1|FL187591
EST:     CCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCAT                         TTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGA
genomic: CCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 84

GCCCGTCCACCGTGCGCGAGGCGCTCTCTCGTGTAGCTACTAGACGACCGCCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 79

GCCCGTCCACCGTGCGCGAGGCGCTCTCTCGTGTAGCTACTAGACGACCGCCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 69

GCCCGTCCACCGTGCGCGAGGCGCTCTCTCGTGTAGCTACTAGACGACCGCCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GCCCGTCCACCGTGCGCGAGGCGCTCTCTCGTGTAGCTACTAGACGACCGCCACCGCCGTCTGGTCTTCGTCGGGTCCTTCGCCGATCAACACCCACCATgtatgtgcat ... ttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttatatgtatacctaataaattcgatttttcctgttctttttgcaaaaagTTATCGGGTGTACATGTGTACACCCATGTCCTACACTGGGTCCGCCCCCGAGCCTTCTGATCCTAACAGGAAACCTG
               acctaat  putative branch site (score: 87)
                         ttcgatttttcctgtt  putative PPT
     ttatatgtatacctaa  TA-rich tract