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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgttgcgcatatactgtattaattagcagccttgcgaaccacagtgactggtactgtttatgctccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG

Basic information

species Zea mays
transcript GRMZM2G145107_T03
intron # 11
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|211075868|gb|FL012538.1|FL012538
EST:     TCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAG                         GTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG
genomic: TCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAGgttcgtgttg ... ccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG




















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), 44 (downstream exon)
Score: 32

GAAGCTGCCTTATGCTTTTGCTGTCAAGCATTGCAGATCACTTACAGCGTTCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAGgttcgtgttg ... ccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 71

GAAGCTGCCTTATGCTTTTGCTGTCAAGCATTGCAGATCACTTACAGCGTTCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAGgttcgtgttg ... ccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 96

GAAGCTGCCTTATGCTTTTGCTGTCAAGCATTGCAGATCACTTACAGCGTTCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAGgttcgtgttg ... ccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 31

GAAGCTGCCTTATGCTTTTGCTGTCAAGCATTGCAGATCACTTACAGCGTTCCGTTTTCTGTGACTGCTGAGCTGACTGCCGGTACAGGAGGTGGACAAGgttcgtgttg ... ccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattagcagccttgcgaaccacagtgactggtactgtttatgctccatctccagGTTTGGCCACAGGAGTCCTAAATCTTGCTATCGTGGTTCCCCAG
 tattaat  putative branch site (score: 31)
                                           ctccatctcc  putative PPT
                                   tgtttat  TA-rich tract