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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTTGTGCTCTCTATCGAAAGCAAACTAAGGATGAACAGGAAGTAAAGGCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttattgggtagttactctctgtatatgtaatgggagtcccctcttcattcatgtttaacttagttagcagttttgcttataattcgcatctttt...

Basic information

species Oryza sativa
transcript LOC_Os01g12180.1
intron # 1
splice site 5'
intron type U2

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|86432563|gb|CI086174.1|CI086174
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88477769|gb|CI415040.1|CI415040
EST:     TGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: TGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|86256002|gb|CI068451.1|CI068451
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88989072|gb|CI042185.1|CI042185
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88484090|gb|CI421361.1|CI421361
EST:     ATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: ATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|87031100|gb|CI259680.1|CI259680
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88962143|gb|CI097296.1|CI097296
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTCGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88502761|gb|CI430267.1|CI430267
EST:     TTTAACCAGATTGATNCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: TTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|86839939|gb|CI332631.1|CI332631
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
EST: gi|88961722|gb|CI096921.1|CI096921
EST:     GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAG                         GGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT
genomic: GCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCT

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: 50 (upstream exon), 42 (downstream exon)
Score: 2

CTGTTTGTGCTCTCTATCGAAAGCAAACTAAGGATGAACAGGAAGTAAAGGCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttat ... atttgtatagGGGATCTTCCATAGCGGAGTTTCTTCTTGATGGTGATACTTTTGGCCCGCTTAAGAAGACTGTCCATGATTTGGAGCAGTACGATCGTTATGCTCTTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTTTGTGCTCTCTATCGAAAGCAAACTAAGGATGAACAGGAAGTAAAGGCCACCATTTTGCATAACAAGCAAGGATTTAACCAGATTGATGCCGCAAGgtatgcttattgggtagttactctctgtatatgtaatgggagtcccctcttcattcatgtttaacttagttagcagttttgcttataattcgcatctttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccctc