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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG

Basic information

species Zea mays
transcript GRMZM2G106795_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106795_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 4
gtctg-tagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG
|| |  ||   | |   | ||   |||| |||    |  ||   || || |   ||| |||  ||       | |||||||||||||  | ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||
gtttaataagctattt-taagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcagGCAATCGTTAATGATCCTTTGATGCTTAACAGTGTAATATTGGTATTTGCCAATAAACAAGATATG
















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|101398288|gb|EB821017.1|EB821017
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCCTGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211076278|gb|FL377992.1|FL377992
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACA
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACA
EST: gi|211066463|gb|FL305323.1|FL305323
EST:     TGATTCATTGGATCGGGAGAGGATTGGAAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATG
genomic: TGATTCATTGGATCGGGAGAGGATTGGAAAA-GCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATG
EST: gi|16925416|gb|BM078484.1|BM078484
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|5714168|gb|AI944153.1|AI944153
EST:     GATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: GATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211066469|gb|FL305329.1|FL305329
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211497259|gb|FL426008.1|FL426008
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGAT
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGAT
EST: gi|211066466|gb|FL305326.1|FL305326
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|14243025|gb|BG840736.2|BG840736
EST:     GGATCGGGAGAGGATTGGAAAAGCTAAAGCTGATTTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: GGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|78088306|gb|DV516699.1|DV516699
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|14242874|gb|BG840205.2|BG840205
EST:     GATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: GATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211531543|gb|FL329354.1|FL329354
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211066462|gb|FL305322.1|FL305322
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTT
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTT
EST: gi|78021877|gb|DV490264.1|DV490264
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211069202|gb|FL305332.1|FL305332
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCC

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), 46 (downstream exon)
Score: 43

ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 157

ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 176

ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 34

ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCCAATAAACAAGATATG
                            agttaat  putative branch site (score: 34)
                                            ttctgtt  putative PPT
         aatttaatttcttcaa  TA-rich tract