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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAAAAGGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaatgcagaactaatttctcagtagtagttatgttggagaagatgaatacagatcatggcgagtcaaagattttcctactaagtgatggctgtcgtattatttag

Basic information

species Zea mays
transcript GRMZM2G052546_T07
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T07 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g01750.5 (Oryza sativa), 5'ss of exon 9
AGTAAAAGGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaatgcagaacta-atttct------------cagta-gtagttatgttggagaagatgaatacagatcatggcgagtcaaagattttcctactaagtgatggctgtcgtattatttag
|||||| | ||||||||||| ||||||||||||||||| ||||| |||||||||||||||||||||  |  | | | ||||||            ||||  ||||||||| |||  ||||| ||       ||  ||  ||  ||   |||  | |||||||||| || || || | |||||
AGTAAACGAGCTTGCTTTCCAAAGTTGGAAGCCATTAAATTGGCTACTGCTGACATTgtaagtgaacactcaccaatatttctttttttttccctcagtgtgtagttatgatggttaagataaa----aggcactgcttgtacaa---ttttgtgctaagtgatgactctcttaatgtttag
















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|21621474|gb|BQ619480.1|BQ619480
EST:     GGCNTTGCTTNNCGA-GTTGGAAGCCATTAAGTTTGCAACTGCTGACATT                         CTGACAGGGAT-ATCCAAAA-CACA-TCACTTTTGAAGTGGGAAGCTGATG
genomic: GGC-TTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGG-ATTATCCAAAAACACAATCACTTT-GAAGTGGGAAGCTGATG
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     GGGCTTGCTTTCCTAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATT                         CTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
genomic: GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
EST: gi|32833578|gb|CD973256.1|CD973256
EST:     GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATT                         CTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
genomic: GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATT                         CTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
genomic: GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
EST: gi|32833853|gb|CD973531.1|CD973531
EST:     GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATT                         CTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
genomic: GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
EST: gi|33091895|gb|CF051889.1|CF051889
EST:     GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATT                         CTAACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT
genomic: GGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaat ... tattatttagCTGACAGGATTATCCAAAAACACAATCACTTTGAAGTGGGAAGCTGATGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAAAAGGGCTTGCTTTCCGAAGTTGGAAGCCATTAAGTTGGCAACTGCTGACATTgtaagtgaatgcagaactaatttctcagtagtagttatgttggagaagatgaatacagatcatggcgagtcaaagattttcctactaagtgatggctgtcgtattatttag

- - - - - - - - - - - -  TGGAAG