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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAAACCTTGTCGGTTATGTTGTAGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcgaattcacatccattatttcatagtgaatttcattcagtcatacggcctcttcagctgacgcctgtgtctattttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g05200.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05200.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G042981_T01 (Zea mays), 5'ss of exon 17
GTGGCAAACCTTGTCGGTTATGTTGTAGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcgaattcacatccattatttcatagtgaatttcattcagtcatacg-------------------gcctcttcagctga-cgcctgtgtc-tattttgcag
|||||||| ||||| ||||| || || || || ||||| |||||| |||| || ||| |||||  |||||||||||||||||| |   |||||||||||    |  |  || ||| |||| ||||| | |                   ||||     | | |   |  || || ||| ||||||
GTGGCAAATCTTGTTGGTTACGTCGTGGGGCCATCCGGGATTAAAGTTCTGATATCAAGAATGGCTGGGAAGGATGgtgagttacagtttcacatccatccacttgtgatggattccatttagtcagatgtacatggcccaactgaacagccttcatggttaaatacacgtttcctatcttgcag
















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|88848612|gb|CI087134.1|CI087134
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88542819|gb|CI472173.1|CI472173
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88532803|gb|CI461436.1|CI461436
EST:     GGACCCTCCGCCATTGAACTTGTCATGTCACGAATGCGTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATGTCATTCTATGTGGGAGTTAAG
genomic: GGACCCTCCGGCATTAAACTTCTCATGTCACGAATGC-TTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|86527322|gb|CI167528.1|CI167528
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88556119|gb|CI486428.1|CI486428
EST:     TGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: TGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|86822518|gb|CI358035.1|CI358035
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|86527366|gb|CI167572.1|CI167572
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88521914|gb|CI449634.1|CI449634
EST:     CATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: CATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88544168|gb|CI474240.1|CI474240
EST:     ACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: ACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88531552|gb|CI460035.1|CI460035
EST:     CCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: CCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|86882287|gb|CI325746.1|CI325746
EST:     GGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: GGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88321005|gb|CI530357.1|CI530357
EST:     AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: AGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88264213|gb|CI367987.1|CI367987
EST:     GACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: GACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
EST: gi|88546313|gb|CI475939.1|CI475939
EST:     TTAAACTTCTCATGTCACGAATGCTTGGGAAGGATG                         CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG
genomic: TTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 52 (upstream exon), 56 (downstream exon)
Score: 3

GTGGCAAACCTTGTCGGTTATGTTGTAGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcg ... tattttgcagCCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCAAACCTTGTCGGTTATGTTGTAGGACCCTCCGGCATTAAACTTCTCATGTCACGAATGCTTGGGAAGGATGgtgagttgcgaattcacatccattatttcatagtgaatttcattcagtcatacggcctcttcagctgacgcctgtgtctattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG