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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttcctggacttctgtatgcctgagattgtatatttatgtatttatgacctcctaattgcttatagcttgtaaaaatctcatttccttttgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG

Basic information

species Zea mays
transcript GRMZM2G023528_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 3'ss of exon 2
acttc--ctggacttctgtatgcctgagattgtatatttatgtatttatgacctcctaattgcttatagc-ttgtaaaaatctcatttccttttgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG
| | |   |  |  |     |   | | |    ||| || | |||| |     |  ||||     | |   ||| ||  || |   || | | | || ||||||| |||||||||||||| || || ||    |||| ||||||||||||||| |||||||| |||||||| || || ||||| |||||||
aatacaattatatattaaccttttttataactcatagttttttatt-accttattttaatgttgcacaatgttgcaacgattta--tttcatctaccatgcagTTTCCTGCACTTCGAGAATTTGTTGGTACAGGAAGGCCTGTCTGGGGAACTTGTGCTGGACTCATCTTCCTAGCTAACAAGGCAGTAG
















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|91055149|gb|EB165567.1|EB165567
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|78120474|gb|DV538858.1|DV538858
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|71437533|gb|DR818583.1|DR818583
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|149073844|gb|EE162166.2|EE162166
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|74233031|gb|DT640945.1|DT640945
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|86472531|gb|DY238901.1|DY238901
EST:     CCGGGGGCGAGAGCCCCACCGTGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCCTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|148986692|gb|EE030480.2|EE030480
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
EST: gi|15100467|gb|BI396258.1|BI396258
EST:     CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAACCTG                         TTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC
genomic: CCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggt ... tgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacctcctaattgcttatagcttgtaaaaatctcatttccttttgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG
      tcctaat  putative branch site (score: 2)
                                tctcatttccttttgc  putative PPT
                          taaaaatctcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttcctggacttctgtatgcctgagattgtatatttatgtatttatgacctcctaattgcttatagcttgtaaaaatctcatttccttttgccctgcagTTCCCTGCACTTCGAGAGTTCGTCGGAGGTGGAAAGCCTGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG

- ttcctgg
- - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat