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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagccactgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG

Basic information

species Zea mays
transcript GRMZM2G361074_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47870.1 (Oryza sativa), 3'ss of exon 3
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagccactgcctcactggactttgaaagaactgacaatctgtttgtattct-tcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
      || |  | || || |||||              | |   ||||       |||     |  || |   |   ||||||| | | | || | |||||| |||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
-gtgttgcttttagtggatattgcattttcgcagtgaattaaatcgagctgtgaagtcaactatccatgtactgatgaacaatctatctttgttgtgtcagGAGTTTGCAACCATGCATTCCACTTCCACTGCATCAGCCGTTGGCTCAAGACCCGTCAAGTGTGCCCTCTAG

upper sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G32060.4 (Glycine max), 3'ss of exon 4
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagcca--ctgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
    ||| ||   ||  |   |||  || |      ||| ||| | |   |  || |   ||| |         |   |  |||    |   | || | ||||| |||| |||||||| || |||||||| || || ||||| ||||| |||||||||||||| || ||||| |
----aaggattttttaaaaagtgcgtag-gtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacaggagTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG

upper sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G32060.3 (Glycine max), 3'ss of exon 3
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagccactgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
                                    ||  ||  | |    || |   ||| |         |   |  |||    |   | || | ||||| |||| |||||||| || |||||||| || || ||||| ||||| |||||||||||||| || ||||| |
------------------------------------ctagta-tatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacaggagtttgtaaccatgcttttcacttccattgcataagCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG

upper sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G32060.1 (Glycine max), 3'ss of exon 3
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagcca--ctgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
   |||| ||   ||  |   |||  || |      ||| ||| | |   |  || |   ||| |         |   |  |||    |   | || | ||||| |||| |||||||| || |||||||| || || ||||| ||||| |||||||||||||| || ||||| |
-tttaaggattttttaaaaagtgcgtag-gtcctttctcctagtatatatatgcttctctacttgttacgttttggcttagcaagagctgaatcttatacagGAGTTTGTAACCATGCTTTTCACTTCCATTGCATAAGCCGATGGCTCAAGACCCGTCAAGTATGTCCTCTAG

upper sequence: GRMZM2G361074_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ06425 (Selaginella moellendorffii), 3'ss of exon 2
tactaagcatgcattgtattttgcaaagcgctgaaactcttagcagagccactgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
                      | ||      |||  |  |   ||  | | ||  |   || ||  || || |    ||| ||| | || ||    ||||  | ||||||||||| || ||||||||||| |||||||| ||||||||||| || ||||| |||||||| |
----------------------gtaaga----gaagatgatcatagctctattggttttgtg-acaatgcaaaac---acactctttgtggat---ccagGCGTGTGCAACCATGCGTTTCACTTCCACTGCATCAGCCGCTGGCTAAAGACTCGCCAAGTCTGCCCTCTCG

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|33285606|gb|CF075401.1|CF075401
EST:     CCAGGCGAACCAGGCGAGCGCCACCAGCGAGGAGTGCACCGTCGCTTGGG                         GAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGA
genomic: CCAGGCGAACCAGGCGAGCGCCACCAGCGAGGAGTGCACCGTCGCTTGGGgtatgattca ... tattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGA
EST: gi|211305108|gb|FL162113.1|FL162113
EST:     GCGAACCAGGCGAGCGCCACCAGCGAGGAGTGCACCGTCGCTTGGG                         GAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGA
genomic: GCGAACCAGGCGAGCGCCACCAGCGAGGAGTGCACCGTCGCTTGGGgtatgattca ... tattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagccactgcctcactggactttgaaagaactgacaatctgtttgtattcttcagGAATTTGCAACCATGCATTCCACTTCCACTGTATCAGCCGTTGGCTAAAGACCCGTCAAGTGTGCCCTCTTG
                            aactgac  putative branch site (score: 2)
                                             tattcttc  putative PPT
                                         tttgtatt  TA-rich tract