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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTCCGCGCGACGCAAAAACCCTAGCCCAGCCACCGACCCCTCTCATGGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccgccggagttcccttgcatctgtttccgctcgattttttccctccttgcggattgtttggctgattgacctggttggtttgcggtatggtggttggcgcag

Basic information

species Zea mays
transcript GRMZM2G085600_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085600_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g62244.1 (Oryza sativa), 5'ss of exon 1
-----ATCATTCCGCG--CGACGCAAAAACCCTAGCCCAGCCACCGACCCCTCTCATGGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccgccggagttcccttg-----catctgtttccgctcgattt-tttccctccttgcggattgtttggctgattgacct---ggttgg-tttgcggtatggtggttggcgcag
     ||  | | |||  || ||||||||||||||||    | ||||    |||||||||  | |||| || |||||||||||||||||| ||||||||||| | ||||||||  |   |  | || |||      | |  ||    | ||  |||    ||||  ||    ||   | |  |||| ||  |   |||||| |||| ||| ||||| |||| ||||
GAATTATTCTCCTGCGCCCGCCGCAAAAACCCTAGCCA---CGCCGA----TCTCATGGCGGCTACCATCAGCCAGGCGAGCCTCCTCCTGCAGAAGCAGCTGAAAGgtgcggatccatgcggctcgcttcgtcctcgttcgtcggtgttctgtttgcgccccttttttttcatccgtggattgatcgatttcggggttgggtttgtggtttggtgattggtgcag
















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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATTCCGCGCGACGCAAAAACCCTAGCCCAGCCACCGACCCCTCTCATGGCAACCACCACCACCCAGGCGAGCCTCCTCCTCCAGAAGCAGCTAAGAGgtgcggcccgccggagttcccttgcatctgtttccgctcgattttttccctccttgcggattgtttggctgattgacctggttggtttgcggtatggtggttggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT