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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgacacgcatcttgagataaaaacccttgcgtttcgttttccttttctttcctttctgaccagtgccatgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG

Basic information

species Zea mays
transcript GRMZM2G019986_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|211384949|gb|FL055084.1|FL055084
EST:     CTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTG                         GTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTG
genomic: CTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTGgtgatgacac ... atgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTG




















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: 83

ACCATGACATCTCACAGCGCTGAAGTCCAAGAAGCTGATGGAAGACATGGCTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTGgtgatgacac ... atgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 71

ACCATGACATCTCACAGCGCTGAAGTCCAAGAAGCTGATGGAAGACATGGCTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTGgtgatgacac ... atgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

ACCATGACATCTCACAGCGCTGAAGTCCAAGAAGCTGATGGAAGACATGGCTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTGgtgatgacac ... atgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 412

ACCATGACATCTCACAGCGCTGAAGTCCAAGAAGCTGATGGAAGACATGGCTGCGCGGGGAGTGAAATACGTAGACTGCTACGGAGTCGACAACGCGCTGgtgatgacac ... atgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccttgcgtttcgttttccttttctttcctttctgaccagtgccatgtctgcagGTTCGAGTTGCGGATCCTACGTTCTTAGGGTACTTCATCGACAAGGGTGTGTCTTCTGCCGCCAAGGTGGTGAGGAAG
                               ttctgac  putative branch site (score: 412)
                    ttttcttt  TA-rich tract