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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTTAGTTCACATGTAAAACTCTTGCTATTTTAATACCACAGGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattacccccttgtgcag

Basic information

species Zea mays
transcript GRMZM2G152775_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152775_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 3
GTTTTTAGTTCACATGTAAAACTCTTGCTATTTTAATACCACAGGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtt-tgctcttcatac--acaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccc-ccttgtgcag
                                            ||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||| | | ||| |  |  | |     |  || |        || ||| || | | | ||    | ||||  | |  |  |||||    | ||   || | |||||||| || ||| || | | |||
--------------------------------------------GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtccccttgaagcgaataggaagaagttgaatgaactcttcatatat-attgttctactagttactggaaacat--ttgatgtgcaagac--agttcatgctaaattttccctccattttcag

upper sequence: GRMZM2G152775_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g53060.2 (Oryza sativa), 5'ss of exon 3
GTTTTTAGTTCACATGTAAAACTCTTGCTATTTTAATACCACAGGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattacccccttgtgcag
                                            ||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||  | | |       || | || |  ||    |||  |||    |  |||||     |                                                              
--------------------------------------------GCTGCTGATACACAAgtaatttccgattatgtacgctattttctccaccaacacacgtaagttgtccccttg-----aagcgaataggaagaagttgaatgaactcttcatatatattgt--------------------------------------------------------------

upper sequence: GRMZM2G152775_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 5'ss of exon 3
GTTTTTAGTTCACATGTAAAACTCTTGCTATTTTAATACCACAGGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgctctt---catacacaacctaac-attaat-----ctcttgtttgataaatcaatat---actgaatgat--------acttaagatctctttgataaatatgatgga---gctgatgctaaaattacccccttgtgcag----------------------------------
                                            ||||| || ||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||    |   | ||  || | ||||||     ||| | ||     ||  |  ||   |||||||||         |  | |||| || || || || |   || |   |  | | ||   | ||    || |||||                                   
--------------------------------------------GCTGCCGACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatttcattaattaacacagtgaactagtagttactgtgaatatttgct-gtgcaagatagcccatgctaaattttccctcgatttgcag

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|32826830|gb|CD966508.1|CD966508
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACC
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACC
EST: gi|32808848|gb|CD961082.1|CD961082
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTA
EST: gi|32826298|gb|CD965976.1|CD965976
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTA
EST: gi|76014048|gb|DT941218.1|DT941218
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAAAAGT-GCAGCCAACTTGATTA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAA-GTTGCAGCCAACTTGATTA

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 1 RNA-Seqlibrary.


Block sizes: 47 (upstream exon), 21 (downstream exon)
Score: 2

GTTTTTAGTTCACATGTAAAACTCTTGCTATTTTAATACCACAGGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAG




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