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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGATCCCACTTTGAAAGCAAATGATGGAGGATATTCATCTGTGCTAGATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgtttgcataaattttaagctttatgcacctgagctcttttttcctaaaaaaatagttttgactggattccttctccag

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 8
splice site 5'
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|20811142|gb|BQ295620.1|BQ295620
EST:     ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAG                         GCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
genomic: ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
EST: gi|31355485|gb|CD439842.1|CD439842
EST:     ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAG                         GCCTCTTCTGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
genomic: ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
EST: gi|22545636|gb|BU097995.1|BU097995
EST:     ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAG                         GCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
genomic: ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
EST: gi|5566802|gb|AI881668.1|AI881668
EST:     ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAG                         GCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
genomic: ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
EST: gi|31361667|gb|CD446024.1|CD446024
EST:     ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAG                         GCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA
genomic: ATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATA

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: 47 (upstream exon), 49 (downstream exon)
Score: 306

TCTGGATCCCACTTTGAAAGCAAATGATGGAGGATATTCATCTGTGCTAGATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATAGCTGCCCCTACGGCTGGACTTCCATCTCAAGCTACTGCAAATCAACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 91

TCTGGATCCCACTTTGAAAGCAAATGATGGAGGATATTCATCTGTGCTAGATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATAGCTGCCCCTACGGCTGGACTTCCATCTCAAGCTACTGCAAATCAACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

TCTGGATCCCACTTTGAAAGCAAATGATGGAGGATATTCATCTGTGCTAGATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATAGCTGCCCCTACGGCTGGACTTCCATCTCAAGCTACTGCAAATCAACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

TCTGGATCCCACTTTGAAAGCAAATGATGGAGGATATTCATCTGTGCTAGATCAGTCACATTCCTTGTTTGATGCACCCTTTGGAATCTCAGGCAACCAGgtagttgcgt ... ccttctccagGCCTCAACAGTAATGTCTGGCCAAGAAACATCGGTTCAACAATCTTCTATAGCTGCCCCTACGGCTGGACTTCCATCTCAAGCTACTGCAAATCAACAAG