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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcggttgatgccgtgatggcctgcttcagctcatctgttcctgtttaagtcctgcttgtctcaccaattggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG

Basic information

species Zea mays
transcript GRMZM2G111713_T02
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|211203210|gb|FL341871.1|FL341871
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAG                         GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATMGGCCACAATCTCG
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
EST: gi|211264640|gb|FL311733.1|FL311733
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAG                         GTTTTDCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
EST: gi|211157788|gb|FL363018.1|FL363018
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAG                         GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGGCCACAATCTC
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATT-GGCCACAATCTC
EST: gi|211337834|gb|FL344315.1|FL344315
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTAT-CGTACGAG                         GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
EST: gi|211474786|gb|FL319644.1|FL319644
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAG                         GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG
EST: gi|211481012|gb|FL352018.1|FL352018
EST:     CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAG                         GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATKGGCCACAATCTCG
genomic: CTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCG

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), 47 (downstream exon)
Score: 78

AGACTACCATGCCTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 51

AGACTACCATGCCTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 44

AGACTACCATGCCTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 51

AGACTACCATGCCTCCGTTTCCCGACCCTTCGCTCCGACCCACACAGGCGTATGCGTACGAGgtgattcggt ... tggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagctcatctgttcctgtttaagtcctgcttgtctcaccaattggcaattagGTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG
                                  gtctcac  putative branch site (score: 51)
                  tgtttaa  TA-rich tract