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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgaaaagaacaattgtatctaaggatgcagcgtgaacttcttgattagaattatgtgggcaggttgtttacagtttgctgctcaattgtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCACAAAAAG

Basic information

species Zea mays
transcript GRMZM2G348866_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348866_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g05650.1 (Oryza sativa), 3'ss of exon 4
ttttgaaaagaacaattgtatctaaggatg-cagcgtgaacttcttgattagaattatgtgggcaggttgtttacagtt---tgctgctcaattgtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCACAAAAAG
| ||   |    | |||  || |  | ||| |   ||  | || ||  | | |||| | ||   |     | |  |||    | |  |||  ||   |  |||| |||||||| || || |||||||| ||||||||||| |||||||||||||| |||||
tcttttca----ctattacatgttggaatgtcctggttcaattatttgtgaaaattttatgaaaatcacttctcaagtcgtgttccactccctttcctcggcagAATACTGAACGCATATGCCAAAGTGCCTCCAAAACCAAAAGTGCCTTCCACGAAAAG
















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|148969459|gb|EE020269.2|EE020269
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|76021487|gb|DT948657.1|DT948657
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|76932642|gb|DV173100.1|DV173100
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|76915823|gb|DV166138.1|DV166138
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|50334180|gb|CO529306.1|CO529306
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|86468761|gb|DY235131.1|DY235131
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|101402261|gb|EB822718.1|EB822718
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|78073578|gb|DV502012.1|DV502012
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|76286853|gb|DV026421.1|DV026421
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|78119406|gb|DV537790.1|DV537790
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|211286797|gb|FL325896.1|FL325896
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|211497313|gb|FL084183.1|FL084183
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|71444517|gb|DR825567.1|DR825567
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|93013298|gb|EB638818.1|EB638818
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAA                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAA
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAA
EST: gi|101396950|gb|EB820400.1|EB820400
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|71449627|gb|DR830677.1|DR830677
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
EST: gi|71447776|gb|DR828826.1|DR828826
EST:     TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAG                         GATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC
genomic: TGGTTTTACAACCAACAGGACTGTGAAGCTGTTGCAAGTCTATTTGGAAGgtaaaggtct ... gtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattagaattatgtgggcaggttgtttacagtttgctgctcaattgtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCACAAAAAG
 tcttgat  putative branch site (score: 4)
                                         aattgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgaaaagaacaattgtatctaaggatgcagcgtgaacttcttgattagaattatgtgggcaggttgtttacagtttgctgctcaattgtattcgcagGATACTGAATGCTTACGCCAAAGTACCTCCAAAACCTAAAGTGCCTTCCACAAAAAG

- - -aaaagaa
- - - - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctc