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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctctgtccacattgaatgctctggttatttggaagttggatctctgctcacctgctgccacctgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCTAGAGCGGCCGTTTATTTTGAGGCAGGCGATTCGTATATTTTCTATAGCG

Basic information

species Zea mays
transcript GRMZM2G438895_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G438895_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g50370.1 (Oryza sativa), 3'ss of exon 7
------------------------gtatgtgct-ctgtccacattgaatgctctggttatttggaagttggatctctgctcacctgctgccacctgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCTAGAGCGGCCG-TTTATTTT-GAGGCAGGCGATTCGTATATT-TTCTATAGCG--
                        |  || | | ||       || |  || |||    |||  |      |  | |||||||| | | || | | |||||||||||||||||||||| |||||||||||||||||||||| |||      ||||  | | |||| |||||||| ||| ||||  ||||||   |  || ||||||   
gattgtttaaacttactgaatttggcttgagttgctccttttcttcatcgcactgacagttttaagc---aaattgtgctcaccggat-ccgcttcttttgcagGATGCTTGGAACAAGTTCACTTCGGAGGAGCGCTAGGATGG-----ATGCTGAAACAGCCGATTTATTTTCGAGACAGGAAATTCGTTAGTAATTATATAGCCAT
















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|13250006|gb|BG360909.1|BG360909
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|60339512|gb|DN206485.1|DN206485
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|60346103|gb|DN213076.1|DN213076
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGG----CGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|33942293|gb|CF348893.1|CF348893
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|67012495|gb|CO441244.1|CO441244
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGG----CGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|4646794|gb|AI621869.1|AI621869
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCT
EST: gi|113814220|gb|DW931581.1|DW931581
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGG
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctggttatttggaagttggatctctgctcacctgctgccacctgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAGGGTGGCGGGGGTGCTAGAGCGGCCGTTTATTTTGAGGCAGGCGATTCGTATATTTTCTATAGCG
                           tgctcac  putative branch site (score: 2)
                                           cctgtttt  putative PPT
       ttattt  TA-rich tract