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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatataactggatcttgatgcgacaaattttgcctcatctttatggactgttattcctatgttctaattgtgcattttgatgtttttcagtatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG

Basic information

species Zea mays
transcript GRMZM2G135568_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135568_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 6
------------aatataactgg-atcttgatgcgacaaattttgcctcatctttatggactgttattcctatgttctaattgtgcattttga--tgtttttcagtatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG
               || | |   | ||   || |  ||   ||       |||| |||  | | | ||    ||| | |  ||| | ||||   | | || ||||||| | | |||||| | |||||||||||||||  | | ||| |||||| |||| |||||||||||||||||||||
ggtgtcacgattgtgatgattattacctctttgtgttaaccattcaactgccttt-tggcttttcaatc----gtttttacagtgtactttggtttatattgcagTATAATTCGGAAAGCTTCTAGTGTCATGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAG
















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|149082655|gb|EE171861.2|EE171861
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGTATAGTCCAG                
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC------A----AGgtactttctt ... t
EST: gi|149061138|gb|EE157398.2|EE157398
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAG                         AAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGAT
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGgtactttctt ... tatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGAT
EST: gi|89249738|gb|DY621524.1|DY621524
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGTATAGTCCAG                
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC------A----AGgtactttctt ... t
EST: gi|149061139|gb|EE157399.2|EE157399
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACA-G                         AAAGCCTGTAGTGTCATGAAA-TATTGAGG
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGgtactttctt ... tatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGG
EST: gi|149083910|gb|EE173286.2|EE173286
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGTCCAG                     
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC-A----AGgtactttctt ... tatagt
EST: gi|88748264|gb|DY532405.1|DY532405
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGTATAGTCCAG                
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC------A----AGgtactttctt ... t
EST: gi|71757754|gb|DR955691.1|DR955691
EST:     TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATACAAGTATAGTCCAG                
genomic: TTGCATGAAGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC------A----AGgtactttctt ... t
EST: gi|60339241|gb|DN206214.1|DN206214
EST:     AGCTCAACAGGAAGTGCACACTCAGCTTGCTCTGGATACAAGTATAGTCCAG                
genomic: AGCTCAACAGGAAGTGCACACTCAGCCTGCTCTGGATAC------A----AGgtactttctt ... t


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgttattcctatgttctaattgtgcattttgatgtttttcagtatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG
                            attttgatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatataactggatcttgatgcgacaaattttgcctcatctttatggactgttattcctatgttctaattgtgcattttgatgtttttcagtatagtccagAAAGCCTGTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - -ctggatc
- - - - - - - ttgatgc
- - - - - - - - - - - - - - - - - - - - - -tggactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt