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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttgcttatctgttgattctgttgggatgccaattttttttatatatttcccgatgaatgactattctatataaattatttgtttaatctttctgcagGGCAATTGTCCTTGCTGTAACAACACTCCTTGATTGGTGGATGTATGGTTCCTGGGTCATAGTGCCGCTTAATTTTTTGAAATTCAACTTATTGTCTTCC

Basic information

species Zea mays
transcript GRMZM2G164175_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 3'ss of exon 3
atgttg-cttatctgttgattctgttgggatgccaattttttttatatatttcccgatgaatgactat-tctatataaattat-ttgtttaatctttctgcagGGCAATTGTCCTTGCTGTAACAACACTCCTTGATTGGTGGATGTATGGTTCCTGGGTCATAGTGCCGC---TTAATTTTTTGAAATTCAACTTATTGTCTTCC
||| ||  |||    ||| || | |||  | | || || || |  |   | ||   ||  | || ||  |||||| |  ||||    |||||| |||||||||||   ||||||||||||| |||||| | |||||||| |||||||||||||||  ||||||||||||||   |||||||||||||||| ||  | || |||   
atgatgatttaaggattgcttttcttgtaaggtcatttgttctctt---tgtcaaaattgaggaatacctctataaaccttatgccttttaatttttctgcagGGTCTTTGTCCTTGCTGTGACAACATTTCTTGATTGTTGGATGTATGGTTCCCAGGTCATAGTGCCGCCACTTAATTTTTTGAAATTTAATCTCTTCTCT---

upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 2
atgttgcttatctgttgattctgttgggatgccaattttttttatatatttcccgatgaatgacta-ttctatataaattatttgttt---aatctttctgcagGGCAATTGTCCTTGCTGTAACAACACTCCTTGATTGGTGGATGTATGGTTCCTGGGTCATAGTGCCGCTTAATTTTTTGAAATTCAACTTATTGTCTTCC
   |   | |    ||| || | |||  | | ||  |||| || |   | || | ||  | || || || |||| |  |||  || ||   ||||| |||||||||   |||||||||| || |||||  | |||||||| ||||||||||||||| || |||||||||| ||||||||||||||||| ||| | || ||||| 
-gatgattgaagcattgcttttcttgtaaggtcatgttttctttt---tctcacaattgaggaatacttttataaaccttacatgctttctaatctgtctgcagGGTCTTTGTCCTTGCCGTGACAACGTTTCTTGATTGTTGGATGTATGGTTCCCGGATCATAGTGCCACTTAATTTTTTGAAATTTAACCTCTTCTCTTCA
















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|211171692|gb|FL201323.1|FL201323
EST:     CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGG                         GGCAATTGTCCTTGC
genomic: CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGGgtaagttatt ... ctttctgcagGGCAATTGTCCTTGC
EST: gi|211171690|gb|FL201321.1|FL201321
EST:     CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGG                         GGCAATTGTCCTT
genomic: CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGGgtaagttatt ... ctttctgcagGGCAATTGTCCTT
EST: gi|211252873|gb|FL444295.1|FL444295
EST:     CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGG                         GGCAATTGTCCT
genomic: CAGATGAAATCAAAATGTTGCTTTATCCTTCTTGATGTCATTCCAGTAGGgtaagttatt ... ctttctgcagGGCAATTGTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttcccgatgaatgactattctatataaattatttgtttaatctttctgcagGGCAATTGTCCTTGCTGTAACAACACTCCTTGATTGGTGGATGTATGGTTCCTGGGTCATAGTGCCGCTTAATTTTTTGAAATTCAACTTATTGTCTTCC
                                      gtttaat  putative branch site (score: 4)
                                            tctttctgc  CT-rich tract
             aatgactattctatat  TA-rich tract