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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCACCGACGGAGGAGGCGGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagaggagattcccttgtgtttgttttttttttctttggtgaaattggatagcttgtcactgcttcactagtggtagtggtaggtagttttttcc...

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 1
GCCCACCGACGGAGGAGGCGGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagaggagattcccttgtgtttgttttttttttctttggtgaaattggatagcttgtcactgcttcactagtggta--gtggtaggtagttttttcc----------
|||| || ||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||| || ||       | || | || |  |||||| ||  ||| ||    |||      || |   | ||   ||||||  |  ||||| |   ||||               
GCCCTCCCACGGAGGAGGCCGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTCGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAATTGGAGgtcagaag------cttccgtatgctccttttttcttatttttgttgttttg------ttctggttcctctcctagtgccatcgtggtggaatgtttgacgtggacgcgtaa

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 1
GCCCACCGACGGAGGAGGCGGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagaggagattcccttgtgtttgttttttt-tttctttggtgaaattggatagcttgtcactgcttcactagtggtagtggtaggtagttttttcc-
|||| |||||||||||||  |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| || ||     ||   |   || |  ||  ||| ||| |||  |    ||   | |||| |         ||  ||  ||   ||   ||  | |  || 
GCCCCCCGACGGAGGAGGTCGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTCGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgttagaagcttccatatgcacatgctccttcatttgtttgtttattagtttttttttgcttcttgaaatgatacctgtcataa--gttcttatatatagcca
















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|88347509|gb|CI637449.1|CI637449
EST:     GACCTCATGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
EST: gi|88573359|gb|CI664930.1|CI664930
EST:     GACCTCATGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     CCAAGGAAGAAC-GGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: CCAAGG-AGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
EST: gi|88342557|gb|CI637133.1|CI637133
EST:     GACCTCATGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
EST: gi|88336064|gb|CI647258.1|CI647258
EST:     GACCTCATGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAG                         AATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC
genomic: GACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagag ... gatttcacagAATTGGCACAGAACATGAGAAGTTCGGTTTTGAAGTTGATACATTGCGTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCACCGACGGAGGAGGCGGTGCAGATGACGGAGCCGCTCACCAAGGAGGACCTCGTGGCCTACCTCGTCTCCGGGTGCAAGCCCAAGGAGAACTGGAGgtgaggagaggagattcccttgtgtttgttttttttttctttggtgaaattggatagcttgtcactgcttcactagtggtagtggtaggtagttttttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA