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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttgcagcctggactcctgtatttacctgtctttagctgtgctgctgaaataaagcatatctcaaacctatcatgcacattttgtttcaattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG

Basic information

species Zea mays
transcript GRMZM2G046587_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 3
-tttcttgcagcctggactcctgtatt-tacctg-tctttagctgtgctgctgaaataaagcatatctcaaacctatcatgcacattttgtttcaattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG
   || ||||| |     || |||| | | |||| ||||||||||   || ||   ||  ||  |  || |  |||| |   ||    || ||   ||||||||||||||| |||||||||||||||||||||||||| |||||||| |||||| ||||||| || |||
tgatcgtgcagaccactttcttgtagtatgcctggtctttagctggattg-tggggtattgctaagttctatgctatgaa--actgcatgatttttttgtcagGTGGTTGAAATTCCTAGAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAG
















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|74244615|gb|DT652529.1|DT652529
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|211349013|gb|FL190902.1|FL190902
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     ACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: ACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|211351406|gb|FL190903.1|FL190903
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|9732830|gb|BE511582.1|BE511582
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|32851273|gb|CD990954.1|CD990954
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GACCAGGGGCTCCTGAATTCTTCAATTGT                         GTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA
genomic: GACCAGGGGCTCCTGAATTCTTCAATTGTgtaagtttac ... caattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgaaataaagcatatctcaaacctatcatgcacattttgtttcaattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG
                                     ttttgtttc  CT-rich tract
                                    attttgtttcaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttgcagcctggactcctgtatttacctgtctttagctgtgctgctgaaataaagcatatctcaaacctatcatgcacattttgtttcaattgtcagGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG