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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttttccctttggttttgttttttgtcattttaaaagaactaccttctctttatctgctaaaatgatattttctgttgtag

Basic information

species Zea mays
transcript GRMZM2G029573_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029573_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 5
ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttttccctttggttttgtttt------ttgtcattttaaaagaactaccttctctttatctgctaaaatgatattttctgt-tgtag
||||||||||||| |||| |||||| |||| |||  | |||||||| ||||||||||||||||      |||     | || ||| ||       |||  | ||||| ||||| ||||  | ||     | |||| || |||| | | | |||||
ATGATGAAGAATCGAACCGATGTTTCCTTGCTGGTCTGATCATAAGGAATCTAAGCATATGgtaaaccattttttcctagtattggttgacataattggaactttaagagaaccacctaatgtt-----gttaaattggtattctttctctgtag
















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|211289805|gb|FL254555.1|FL254555
EST:     ATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: ATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|31355937|gb|CD440294.1|CD440294
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|31361816|gb|CD446173.1|CD446173
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|89248122|gb|DY619908.1|DY619908
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCCACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|148969434|gb|EE020234.2|EE020234
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|211518587|gb|FL052555.1|FL052555
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|211289807|gb|FL254557.1|FL254557
EST:     TCAAACCAATGTTT-CTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGAT
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGAT
EST: gi|71764310|gb|DR962247.1|DR962247
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|211287670|gb|FL254548.1|FL254548
EST:     TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: TCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
EST: gi|211287673|gb|FL254551.1|FL254551
EST:     ATCTAAGCATATG                         TACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG
genomic: ATCTAAGCATATGgttggttttt ... tctgttgtagTACTTCCAACTGGCGATGCAAAGAAACACTTGAGAAGTATCTGATTAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATGgttggttttttccctttggttttgttttttgtcattttaaaagaactaccttctctttatctgctaaaatgatattttctgttgtag

- - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - -  AAGAAA