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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtgattacatatgtacttgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA

Basic information

species Zea mays
transcript GRMZM2G005308_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g04010.1 (Oryza sativa), 3'ss of exon 8
tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtga--ttacatatgtact-tgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
  | | |||     | || |  ||| ||  ||      | |||| ||   ||||  |||  ||  |    | ||      |   ||    |||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| 
-aaatttgttcccaccattt-cattggtgctttatgcat-attttttcccctgtaatgatattggaggcttgctgcattgacctaacttttgtttccacttagGCAAATACCTTATTTAAGAGAATATGCTTGAAGTTGGATGCACTATCTCATTTCCACTTTGCTCCAAAGCCG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g04200.1 (Oryza sativa), 3'ss of exon 8
tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtga--ttacatatgtact-tgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
  | | |||     | || |  ||| ||  ||      |  ||| ||   ||||  |||  ||| |    | ||      |   ||   ||||||| || |||||||| || ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| 
--aatttgttcccaccattt-cattggtgctttatgcatatttttttcccctgtgatgatattagaggcttgctgcattgacctaacttctgtttccacttagGCAAAGACCTTATTTAAGAGAATATGCTTGAAGTTGGATGCACTATCTCATTTCCACTTTGCTCCAAAGCCG
















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|60347217|gb|DN214190.1|DN214190
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211462206|gb|FL207483.1|FL207483
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211459691|gb|FL207478.1|FL207478
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|24769907|gb|CA405036.1|CA405036
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211183290|gb|FL434310.1|FL434310
EST:     AGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: AGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|60394413|gb|DN227283.1|DN227283
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|71764578|gb|DR962515.1|DR962515
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|71761969|gb|DR959906.1|DR959906
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211183291|gb|FL434311.1|FL434311
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|31364214|gb|CD448569.1|CD448569
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211462204|gb|FL207481.1|FL207481
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|76011806|gb|DT938976.1|DT938976
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|40303495|gb|CK347882.1|CK347882
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|37392792|gb|CF633649.1|CF633649
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgttgtgattacatatgtacttgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
                                   gaataac  putative branch site (score: 2)
                                            tttctacct  putative PPT
                               taatgaataa  TA-rich tract