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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGAGGTGGAGGAGGAGACGAGCGCGTGGTGGTGGTGGTGTTGGCGGCGATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctccccgttcctcgtttggatctgtgcttgcgcgcgcttagatttgtctatttgatgttgtgctggagttcgatctaagatgggctgtgaatg...

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 1
GAGAGAGGTGGAGGAGGAGACGAGC-GCGTGGTGGTGGTGGTGTTGGCGGCGATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctccccgttc--ctcgtttggatctgtgcttgcgcgcgcttagatttgtctattt-gatgttgtgctggagttcgatctaagatgggctgtgaatg-
 || |||  ||  | |    || || ||||    |||||| || || |||| |||||||||||||| |||| ||||||||||||||||||||||||||||||| | |  | | ||| |   ||| ||     |  |  |  |   | ||   ||||| | ||| | | || |  |   ||  ||| | ||||| | | ||  || 
-AGGGAGAAGGGCGCGCGCGCGCGCAGCGTTCAAGTGGTGCTGGTGTCGGCCATGGATCGGGTTCGTGGATCCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtaccacatgctcgtgcgattcggtttctcttaagtatttgtttgttt--gtttgtttgttttgttattata-tactgtgagatgtgagatgagatctgg-tgc

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 1
GAGAGAGGTGGAGGAGGAGACGAGCG-CGTGGTGGTGGTGGTGTTGGCGGCGATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatct------ccccgtt-cctcgtttggatctgtgcttgcgcgcgcttagatttgtctatttgatgttgtgctggagttcgatctaagatgggctgtgaatg
  |  ||| |  |   | |   |||| || |||| |||||  | || || | |||||||||| |||||||| ||||||||||||||||||||||||||||||| |   |       ||||||  ||||||  || |||||      | |   ||   ||||  | ||| || || || |   ||  ||| |   ||||  || ||   
-CGGAAGGCGAGGCGCGCGCGCAGCGTCGAGGTGCTGGTGCCGGTGCCGCCCATGGATCGGGCTCGCGGATCCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtacctaccatgcgaccccgtcgcctcgtgcggttctgtttccatgagttttt---tttgcttgttttat-ttatgttactgtgagatatgttatggcatgaga---
















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|29624638|gb|CB629649.1|CB629649
EST:     GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|1631642|gb|C19371.1|C19371
EST:     ATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTNCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: ATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|29630263|gb|CB635272.1|CB635272
EST:     GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|396941184|gb|HO188393.1|HO188393
EST:     GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCAAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|29630765|gb|CB635774.1|CB635774
EST:     CGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTTCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: CGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|570171|gb|D41020.1|D41020
EST:     GATGGATCGGGTTCGCGGATGCGCGTNCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|29628702|gb|CB633713.1|CB633713
EST:     GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
EST: gi|29630767|gb|CB635776.1|CB635776
EST:     GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAG                         GATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA
genomic: GATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTA

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: 75 (upstream exon), 75 (downstream exon)
Score: 201

GAGAGAGGTGGAGGAGGAGACGAGCGCGTGGTGGTGGTGGTGTTGGCGGCGATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctc ... ctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTACCGTGATCGGTATTGATCTTGGTACAACCTACTCGTGTGTCGGTGTGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGAGGTGGAGGAGGAGACGAGCGCGTGGTGGTGGTGGTGTTGGCGGCGATGGATCGGGTTCGCGGATGCGCGTTCCTGCTCGGCGTCCTGCTCGCAGgtgcgatctccccgttcctcgtttggatctgtgcttgcgcgcgcttagatttgtctatttgatgttgtgctggagttcgatctaagatgggctgtgaatg

- - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccg