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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttacttattgaggttgtcatttttgataaattttgttgcattcgagtggcctgactcccgtgagctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA

Basic information

species Zea mays
transcript GRMZM2G045241_T05
intron # 13
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|76294030|gb|DV033598.1|DV033598
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|32797227|gb|CD949463.1|CD949463
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|78081455|gb|DV509867.1|DV509867
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|32799719|gb|CD951955.1|CD951955
EST:     CCCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|76908596|gb|DV163020.1|DV163020
EST:     CAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|32800743|gb|CD952979.1|CD952979
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|32800292|gb|CD952528.1|CD952528
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
EST: gi|78117446|gb|DV535833.1|DV535833
EST:     CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAAT                         GTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA
genomic: CTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACA

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), 49 (downstream exon)
Score: 114

CAACTTTGTTCCTGGGATCCTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA


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

CAACTTTGTTCCTGGGATCCTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

CAACTTTGTTCCTGGGATCCTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 199

CAACTTTGTTCCTGGGATCCTCGAAGGAGGCCAACTGCTGAGCAAGCATTACAACATCCTTTCTTCAATgtactgttac ... agctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttgataaattttgttgcattcgagtggcctgactcccgtgagctttctagGTGTGCAATTGGGTACCAAGACCTGTACATGATGCTTACCATACAAAAACAAACGGACCTA
                               gcctgac  putative branch site (score: 199)
                                               ctttct  putative PPT
     ttgataaattttgtt  TA-rich tract