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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattcttcacccacctacatttcaatgttatatcggtatctatcacacgtaatggctgcaattgaatgagttttttttttctatcaagtgttgcgcctctataaccttcctgtgcttgttaatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC

Basic information

species Zea mays
transcript GRMZM2G412234_T01
intron # 10
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|32930111|gb|CF034923.1|CF034923
EST:     GCCTTGCTCGTGTGTATGCATTGTGGAACATAACTCCACTGGCCAATGTT                         GTTGTGGCTTTCATATGTGGTTTTGT
genomic: GCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGT
EST: gi|32916793|gb|CF021605.1|CF021605
EST:     GCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGAT                         GTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACA
genomic: GCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACA

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), 47 (downstream exon)
Score: 61

TCCTGCCGGTATAAATGCTCTATTTAGTCATGGACCGAGGCGGTCAGCAGGCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

TCCTGCCGGTATAAATGCTCTATTTAGTCATGGACCGAGGCGGTCAGCAGGCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

TCCTGCCGGTATAAATGCTCTATTTAGTCATGGACCGAGGCGGTCAGCAGGCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TCCTGCCGGTATAAATGCTCTATTTAGTCATGGACCGAGGCGGTCAGCAGGCCTTGCTCGTGTGTATGCATTGTGGAACATAACTTCACTGGTCAATGTTgtaagtattc ... taatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttctatcaagtgttgcgcctctataaccttcctgtgcttgttaatatctagGTTGTGGCTTTCATATGTGGTTTTGTACATTATAAGTTATCAACCAAAACACACCCGAGCGTGCAGCCCTGGAACCTGGGAAC
                                          tgttaat  putative branch site (score: 134)
                                         ttgttaatat  TA-rich tract