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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtagttcttttttgcattgccattcctccccatctcgattgtatacttctggtatagtatgttggaaggctaatgctgaaatcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA

Basic information

species Zea mays
transcript GRMZM2G071304_T01
intron # 15
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|67020482|gb|CO449231.1|CO449231
EST:     GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG                         GGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC
genomic: GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC
EST: gi|211137634|gb|FL282503.1|FL282503
EST:     GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG                         GGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC
genomic: GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC
EST: gi|18661332|gb|BM501358.1|BM501358
EST:     GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG                         GGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC
genomic: GCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGC

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: 86

GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 11

GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 9

GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAGgtctgtagtt ... atcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgtatacttctggtatagtatgttggaaggctaatgctgaaatcgaaccagGGTATCTCTCTAAGATTCCCTCGCCTATTGAGATTACGTGACGATAAAAGCCCAGAACAAGCCACCACGTCTGACCAA
                                ggctaat  putative branch site (score: 9)
                 tatagtat  TA-rich tract