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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggcccgccggagttcccttgcatctgtttccgctcgattttttccctccttgcggattgtttggctgattgacctggttggtttgcggtatggtggttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCT

Basic information

species Zea mays
transcript GRMZM2G085600_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62244.1 (Oryza sativa), 3'ss of exon 1
----------gtgcggcccgccggagttcccttgcatctgt-ttccgctcgattttttccctccttgcggattgtttggctgattgacctggttggtttgcggtatggtggttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCT
           |||||| |||    || | | | | || || ||| | | |      |   |  |      | | |||   ||||     | | |||||| ||| ||||| |||| |||||||||||||||||||| |||||||||||||| |||||| | |||||||||||||| |||||||||||||||||||| |||||||| ||||||||||||||
gtgcggatccatgcggctcgcttc-gtcctcgttcgtcggtgttctgtttgcgccccttttttttcatccgtggattgatcgatttcggggttgggtttgtggtttggtgattggtgcagATCTCGCGAAGCACCCCGTGGATGGGTTCTCGGCTGGGTTAGTCGACGACAGCAACGTCTTCGAGTGGCAGGTCACAATCATCGGCCCGCCTGACACCCT

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 1
lower sequence: EDP03036 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtgcggcccgccggagttcccttgcatctgtttccgctcgattttttccctccttgcggattgtttggctgattgacctggttggtttgcggtatggtggttggc--gcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCT
                                           |   ||    | || |          |||   | |      |     | | | | |    ||  ||||| ||| | | | |||| |||||||| ||||| ||||| || ||||| || ||||| || ||||||||||||||||||||||| || || || || || ||
------------------------------------------gtgcgccggtttcgcaggcgcgacacttgagcaaacc--ccagacgaagctctcgcgccctgcccgcagAGCTCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACT
















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|211533490|gb|FK952750.1|FK952750
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCG-AMSACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211533488|gb|FK952748.1|FK952748
EST:     GGCAACCACCACCACCCAGGCGAKHCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAM--ACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211533484|gb|FK952744.1|FK952744
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211533493|gb|FK952753.1|FK952753
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211530484|gb|FK952736.1|FK952736
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211313830|gb|FL083564.1|FL083564
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCCGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211533486|gb|FK952746.1|FK952746
EST:     -GCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211315846|gb|FL083573.1|FL083573
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCCGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211530487|gb|FK952739.1|FK952739
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|74240335|gb|DT648249.1|DT648249
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211530485|gb|FK952737.1|FK952737
EST:     GGCAACCACCACCACCCANGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCG-AMSACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
EST: gi|211533485|gb|FK952745.1|FK952745
EST:     GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAG                         ATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA
genomic: GGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccg ... gttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcggattgtttggctgattgacctggttggtttgcggtatggtggttggcgcagATCTCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCT
                gattgac  putative branch site (score: 3)
     attgttt  TA-rich tract