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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtcgatttaatctctcagttgacatgctgacattattgttgttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT

Basic information

species Zea mays
transcript GRMZM2G087144_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g35960.1 (Oryza sativa), 3'ss of exon 1
tactgtcgatttaatctctcagttgacatgctgacattat-tgttgttgatc--tatctgactgagtataccatttgctggaa-tatacccta-tatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
        | ||| ||| |||||||  |||      |||| | || ||||||  |||||  ||   |   ||| || ||  || ||| |  || | |  || |||||||||  | || ||||||||||| || |||||||||||||||| |||||||||| |||| |||||  || ||||||| || |||||||| |||||||||
-----attagttagtctgtcagttggtatggcagtgttatcttttattgatccatatcttccttgttgctccactttctaaaactattctttaatcttctttcagGGGTGGAATAAAGTCTCCATGGTCTCGAAGGAAAAGAAAACGAGTACTTTCTCGTCAACAATGGGAAGGTCTGTTTTCTGCTAATGGGAAACTTCGTGAT

upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G13850.1 (Glycine max), 3'ss of exon 1
tactgtcgatttaa-tctctcagttgacatgctgac-attat-tgttgttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
| || ||  | ||| | ||| |  |||  ||||| | ||| | | || |  |  |  || ||      ||  |||   |  |||         | | || ||||||| |||||||||| |||||||| || |||||||||||||  |  ||  | | | | || ||| | || |||||| |   | ||||||   | || |||
tcctttcactctaaatttcttaaatgat-tgctgcctattctctattctaaaattgacttacaagcagtaatattgaat--aattcttttggcaaaatttcagGGGTCGTCTTAAATCACCATGGTCACGCAGGAAAAGAAAACATGTCCTAACACCTCAGCAATGGAAAAGCTTGTTTACCCAAGATGGGAGAATACGGGAT

upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G41000.1 (Glycine max), 3'ss of exon 1
tactgtcgatttaatctctcagttgacatgctgacattattgttgttgatctatctgactgagta-taccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
   |   ||||  | | |       ||| |    ||  |      || | |  |       || | ||  |||   |  | ||        | | || ||||||| |||||||||| |||||||| || |||||||||||||  |  ||| | | | | || ||| | ||  ||||| |     ||||||   | || |||
gtttccggattcgaacccatgaccaacaggtcaccaagacacaactttaccgctgcatacaagcagtaatattgaata-attacttttggcaaaatttcagGGGTCGTCTTAAATCACCATGGTCACGCAGGAAAAGAAAACATGTCCTTACACCTCAGCAATGGAAAAGCGTGTTTACCCAGGATGGGAGAATACGGGAT

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|148981030|gb|EE027393.2|EE027393
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211081607|gb|FL369112.1|FL369112
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211426207|gb|FL392504.1|FL392504
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGG
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGG
EST: gi|211076165|gb|FL369890.1|FL369890
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGATAAGA
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGA
EST: gi|50332287|gb|CO527413.1|CO527413
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211469235|gb|FL410783.1|FL410783
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCYTAAATCTCCATGGTCCCGGAGGAAAAGAA
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAA
EST: gi|211097332|gb|FL386847.1|FL386847
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211397522|gb|FL373465.1|FL373465
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         NNGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211392710|gb|FL395249.1|FL395249
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211476313|gb|FL383250.1|FL383250
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAAGAAAAGAAA-CGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211082072|gb|FL392684.1|FL392684
EST:     CCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGNAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGGAAAGAAA-CGAGCACTTT
genomic: CCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGG-AGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
       atctgac  putative branch site (score: 3)
                                          tatatatttaca  TA-rich tract