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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGGTCTGCCTCCTTGGA

Basic information

species Zea mays
transcript GRMZM2G122039_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122039_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 1
ttcactgcacaacgg--ccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctct-atctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGGTCTGCCTCCTTGGA
    ||||     |    |    |    |   || || |         |  | | ||||  |   |  | |||  |  | |    || |||   | ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||               
---gctgcctgctgagttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG---------------

upper sequence: GRMZM2G122039_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGGTCTGCCTCCTTGGA
                                                             | |  ||  |  | ||  || || | |  | | || |         |  | | ||||  | | |    || |||   ||   | | |  |   ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||               
gttggtttaattttggtacttcaatgtaattgtggtgtcaccatcaatagcttccgccgactgctgtgttcttctgcttgt-gttattttacttttcttttttatggcattctctcctatt-tattgcatttcatttgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTAGAATACCAG---------------
















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|56382672|gb|CV985341.1|CV985341
EST:     CGACCTGGTGGTGTGCACGGCTGATTGGTCGCTGCTTCAGTCATGAGAGG                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGACCTGGTGGTGTGCACGGCTGATTGGTCGCTGCTTCAGTCATGAGAGGgtaatgcttt ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGGTCTGCCTCCTTGGA
                                 tcctaat  putative branch site (score: 2)
                                            ctctatctc  putative PPT
                                    taatgtt  TA-rich tract