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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctctcgcgacgaacagagccgagcatagcctcctcctcctcctgttcttgatttggtgtgtctcgcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTCACCGACCTCGACCTCGTCATCTCCAAGTCGTACATCTGCTCCGACGGCG

Basic information

species Zea mays
transcript GRMZM5G839349_T01
intron # 2
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|148954551|gb|EC899989.2|EC899989
EST:     GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAG                         GTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTC
genomic: GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAGgtttgctctc ... gcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTC
EST: gi|148945599|gb|EC890853.2|EC890853
EST:     GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAG                         GTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTC
genomic: GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAGgtttgctctc ... gcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTC

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 3 RNA-Seq libraries.


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 1

GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAGgtttgctctc ... gcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTCACCGACCTCGACCTCGTCATCTCCAAGTCGTACATCTGCTCCGACGGCG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAGgtttgctctc ... gcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTCACCGACCTCGACCTCGTCATCTCCAAGTCGTACATCTGCTCCGACGGCG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 21

GGTCGTCGTCGATAACGAGACGCGCGAGGACTGCACGCTCGTCAAGgtttgctctc ... gcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTCACCGACCTCGACCTCGTCATCTCCAAGTCGTACATCTGCTCCGACGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagcatagcctcctcctcctcctgttcttgatttggtgtgtctcgcgttcccagGTCGACAGCGTGAACCGGGACGGCGTGCTGCTGGACATGGTGCAGCTGCTCACCGACCTCGACCTCGTCATCTCCAAGTCGTACATCTGCTCCGACGGCG
                          tcttgat  putative branch site (score: 21)
                                              cgttccc  putative PPT
                            ttgattt  TA-rich tract