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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcagctccctcgatcatccctcgtcaccattttttccggccatcaatcaagtaaaaaaatggaaacgcaacgcag

Basic information

species Zea mays
transcript GRMZM2G131650_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131650_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g07764.1 (Oryza sativa), 5'ss of exon 4
--------CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcagctccctcgatcatccctcgtcaccattttt----tccggcca-tcaatcaag--taaaaaaatggaaacgcaacgcag----------------
         |||| |  ||||   ||  ||| |  |  | ||  |   ||||   ||| | | | |||      || |||   || ||    | ||     | |||  | | | ||  |    ||  |  |  |||  | || ||| |       |  || ||||||| |  ||   |  | | | |      |||                
GGCGAAGGTGGCGTCGCCGGCG--GAGTTCAGCCTCTCCCAGATC---TGGC---TCATCTC-CGGCTCCTT--CGGCAATGACCTCAACACCATCGAG-GCCGGATGGCAGgtgctacattttcttttctttctctcctccttttctgaaacttgttcagtcaatcaggcctagctagctagtagccagtttcagagattacattttactc

upper sequence: GRMZM2G131650_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g07764.1 (Oryza sativa), 5'ss of exon 5
CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagca--gctccctcgatcatccctcgtcaccattttttccg-gccatcaatcaagtaaaaaaatggaaacgcaacgcag---------------------------
                                              || ||||||||||||||||| ||||||| ||| ||||||||||| || |||||||||||  |   |||       |  |     ||  | | | |||| |    |  |   |  || |  | |     |  |   ||                            
----------------------------------------------GTGAGCCCTCAGCTGTACGGTGACAACAACCCAAGGTTCTTCACGTATTGGACAgtaagttctttgctagtaaagtagtaatctgttcctagtgtttcagtattagaagagagatagatcagtcagttcaaagaacaagttactgaagaatgatgcattgtgcag
















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|76010479|gb|DT937649.1|DT937649
EST:     GCCTTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|12046190|gb|BF728329.1|BF728329
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|86474297|gb|DY240667.1|DY240667
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|78180215|gb|DV550588.1|DV550588
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|6827523|gb|AW331166.1|AW331166
EST:     GCCCTCAGCTGGACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGCCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|149076068|gb|EE164645.2|EE164645
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcagctccctcgatcatccctcgtcaccattttttccggccatcaatcaagtaaaaaaatggaaacgcaacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG