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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctaatcgcatcttcaacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTG

Basic information

species Zea mays
transcript GRMZM2G020574_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
-------gtttgtc-taatcgcatcttcaacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTG
        || ||    || |||| || |  | ||  ||| ||| ||| |  |  |||  ||  |||  ||| ||   | |||||||| ||||| ||| |||||||||||||||||||||||||||| |||||||| ||||||||||||                      
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG----------------------

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtttgtctaatcgcatcttcaacagtgctaatacttatagaaa---cacaattagtgactaaacaattatctctata-gATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTG
                         ||  || |    |    || |  |||    |  |   |      ||   ||| |   |   ||||||| | | || |||||| ||||| ||||||| |||  |||||||||||||||| ||  | ||||| ||||||||||||                      
gtttgtcctattcagtgtttgcaaattaacttaaaagacacacacctttgcatgcatgtgccgttgtttcaagcttaatt-tttggcaattatgtttttaagATGCTCGGAGTGAAGCGAATTGAGCGGGTTCTTCCAACTGGCACACCTTTGACTGTTGTTGGTGAG----------------------
















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|149085186|gb|EE174691.2|EE174691
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGGACCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTG
EST: gi|149112302|gb|EE295197.2|EE295197
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTG
EST: gi|76917346|gb|DV166781.1|DV166781
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtgctaatacttatagaaacacaattagtgactaaacaattatctctatagATGCTGGGAGTAAAGCGAACTGAAAGGGTTCTTCCAACTGGAACCTCATTGACAGTTGTTGGTGAGGTATTATTTCTATTATCCATTG
                                 gactaaa  putative branch site (score: 2)
                                           ttatctct  putative PPT
        taatacttatagaaa  TA-rich tract