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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAAACGAGTCGATCCAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttttttctgcaattatcttatatttttaaaacaaatgtggtctctagattttctcatactgagcatatttgcttgctgtttataatgaagtgcttatcctatgttgaaactactgctcaatcattatgtgtttggaccctcag

Basic information

species Zea mays
transcript GRMZM5G870572_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 5'ss of exon 11
ATAAAACGAGTCGATCCAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttttttctgcaattatcttatatttttaaaacaaatgtggtctctag--attttctcatactgagcatatttgcttgctgtttataatgaagtgcttatcctatgttgaaactactgctcaatcattatgtgtttggaccctcag
|||||||||||||||||||||||||| |||||||||||  |||||||||| ||||| |||||||||||  |  | | ||||  | || | ||  || |  ||    | ||  | |   ||  || |     || ||||||    |   || | ||| ||  |||      ||| |  ||||    | ||| |     | ||| |  |||| |    ||
ATAAAACGAGTCGATCCAACATTAGATATGGAGGCAGATGCTGGAGATGACTACATCCATCTTCCGgtgcgtctgtattctctacttctgttgcatatgcaacttga-tgaagacgaaagtgatatatctttattgagcaaggatatctgttctttttatcgaa------atcatgagttgcttatcctgttttgataatattttgttgggcatgtag

upper sequence: GRMZM5G870572_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G33940.1 (Glycine max), 5'ss of exon 11
ATAAAACGAGTCGATCCAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttttttctgcaattatcttatatttttaaaacaaatgtggtctc----tagattttctcatactgagcatatttgcttgctgtttataatgaagtgcttatcctatgttgaaactactgctcaatcattatgtgtttggaccctcag
 |   ||| || |||||||| ||||||||||| ||||||   |||||||||||||  |||||||| ||||| |   |    | || |||     | | | | |    | ||  | ||     |  |||| ||||| |    ||      |  |  |||||| || |    |                                                 
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaat----gaaactattcctcaatctcatataggaggttctttcacagcatgttttttcatatt--ttatgcaaattcaccttttatagtgtaaaattg------------------------------------------------
















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|74239225|gb|DT647139.1|DT647139
EST:     CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCG                         GACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTCGATGCTGACAGT
genomic: CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttt ... ggaccctcagGACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTCGATGCTGACAGT
EST: gi|211184532|gb|FL153187.1|FL153187
EST:     AACATTAGACATGGAGGCAGACACTGGGAGATGATTACATTCATCTTCCG                         GAACATGGGATTTCACCGTGATGGTAGCAAAGAGACAGTCGATGCCTGACA
genomic: AACATTAGACATGGAGGCAGACACTGG-AGATGATTACATTCATCTTCCGgtatgatttt ... ggaccctcagGACCATGGGATT-CACCGTGATGGTAGCAAAGAGACAGTCGATGC-TGACA
EST: gi|31356392|gb|CD440749.1|CD440749
EST:     CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCG                         GACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTCGATGCTGACAGT
genomic: CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttt ... ggaccctcagGACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTCGATGCTGACAGT
EST: gi|13150541|gb|BG320863.1|BG320863
EST:     CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCG                         GACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTTGATGCTGACAGT
genomic: CAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttt ... ggaccctcagGACCATGGGATTCACCGTGATGGTAGCAAAGAGACAGTCGATGCTGACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAACGAGTCGATCCAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttttttctgcaattatcttatatttttaaaacaaatgtggtctctagattttctcatactgagcatatttgcttgctgtttataatgaagtgcttatcctatgttgaaactactgctcaatcattatgtgtttggaccctcag

- - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - -  GAGATG