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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattccttcattatacaactggattctgttaaaaactctttcttgttctgatatgtttggaattttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAA

Basic information

species Zea mays
transcript GRMZM2G132712_T01
intron # 29
splice site 3'
intron type U2

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|5846745|gb|AI999828.1|AI999828
EST:     GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG                         GCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
genomic: GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttagtattc ... ttttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
EST: gi|5296205|gb|AI782885.1|AI782885
EST:     GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG                         GCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
genomic: GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttagtattc ... ttttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
EST: gi|6020890|gb|AW065818.1|AW065818
EST:     GGAACCTCTTGTTACAAATATCATGAGGAGAAACTTGTTTGNTCAG                         GCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
genomic: GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttagtattc ... ttttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
EST: gi|60340338|gb|DN207311.1|DN207311
EST:     GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG                         GCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
genomic: GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttagtattc ... ttttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGG
EST: gi|116821995|gb|EC865361.1|EC865361
EST:     GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG                         GCCCTTTACCAAGTAGCAATTCTATCTGATTTTCGATTTTGATGGAGTAAG
genomic: GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttagtattc ... ttttacacagGCCCTTTACCAAGTAGCAATTCT-TCTGATTTTCGATTTTGATGGAGTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggattctgttaaaaactctttcttgttctgatatgtttggaattttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAA
                            ttctgat  putative branch site (score: 3)
         tgttaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtattccttcattatacaactggattctgttaaaaactctttcttgttctgatatgtttggaattttacacagGCCCTTTACCAAGTAGCAATTCTTCTGATTTTCGATTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG