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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACCTTAGACAAATTGCTCAAGAAACAAGTGGAGAAGTAGTGTATGCCTTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttttattgaactttaaccccgactttcatgtacatcttgctgtctagtttaaaacataaaagtctcttgttcttccattag

Basic information

species Zea mays
transcript GRMZM2G042250_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042250_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 5'ss of exon 11
GCCACCTTAGACAAATTGCTCAAGAAACAAGTGGAGAAGTAGTGTATGCCTTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttttattgaactttaaccccgactttcatgtacatcttgc-tgtctagtttaaaacataaaagtctcttgttcttccattag
| ||| | |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||| ||||| |||||||| ||||||||||| || ||||||| ||||||||||  || | | || | |   || || |   | |  | ||| || | ||| ||  || | | |  | |||||       
GGCACATCAGACAAATTGCTCAAGAAACAAGTGGGGAAGTGGTGTATGCCTTGGGGAGGCAACCAGCAGTGCTACGGACTTTTAGTCAAAGGCTGAGCAGgtgatttttttat-aaattattactcagcaattaatatttttttcacctgtttaatctaacac-caatattatgcttttcttag-----

upper sequence: GRMZM2G042250_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 10
GCCACCTTAGACAAATTGCTCAAGAAACAAGTGGAGAAGTAGTGTATGCCTTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttttattgaactttaaccccgactttcatgtacatcttgctgtctagtttaaaacataaaagtctcttgttcttccattag
|  |  | || ||| | || |||||  | | ||| |||||||||||||  || |||||||| ||||| |||||  | |||||||| |||||| ||||||||||  ||   | |||| ||  ||||      ||| |        || |  ||  ||   |   |    || ||||| | |||    ||
GGTATATCAGGCAATTAGCCCAAGAGTCTAATGGTGAAGTAGTGTATGGATTAGGAAGGCAGCCTGCTGTTCTTAGAACCTTTAGCCAAAGATTAAGCAGgta-cttcgatcttgagctaaaacctaattgttctt---tgctctgtttgctcattgtcattttttctgt-tcttggttttcttgaag
















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|71422277|gb|DR805676.1|DR805676
EST:     TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAG                         GGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT
genomic: TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttt ... cttccattagGGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT
EST: gi|211357660|gb|FL143935.1|FL143935
EST:     TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAG                         GGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT
genomic: TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttt ... cttccattagGGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT
EST: gi|60340950|gb|DN207923.1|DN207923
EST:     TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAG                         GGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT
genomic: TTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttt ... cttccattagGGGGTTTAATGATGCCATTAGTGGTTTCAACGATGATGGTTGGTCTGTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACCTTAGACAAATTGCTCAAGAAACAAGTGGAGAAGTAGTGTATGCCTTGGGAAGGCAACCTGCAGTTCTACGGACCTTTAGTCAAAGACTAAGCAGgtaatttttttattgaactttaaccccgactttcatgtacatcttgctgtctagtttaaaacataaaagtctcttgttcttccattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG