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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACAGGCTGCTGAACAAACTGTTGATGAAACTAGCGTTCAAACTCTTGTTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatcttctgtttttaatttcatccatgatagttgatcttttacattttcttgtacagttcgcaatgttgaatacctctcagaaagttgatatttg...

Basic information

species Oryza sativa
transcript LOC_Os01g08200.1
intron # 17
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|86479384|gb|CI122017.1|CI122017
EST:     TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGCCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|86481792|gb|CI124425.1|CI124425
EST:     AAGATGTTGCTCGAAAGGCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCGTGAGGCT
genomic: AAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|88837959|gb|CI371537.1|CI371537
EST:     TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCT                         GGTGGATATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|88982976|gb|CI250580.1|CI250580
EST:     AAGGCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: AAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|3768668|gb|AU032695.1|AU032695
EST:     AGATGTTGCTCGAAAGCCCTTGGCAGCTTCT                         GGTGG-AATNTCGAGAGNGCAACAGACTGGATTTTTNGCCNCCCTGAGGCT
genomic: AGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|29622185|gb|CB627196.1|CB627196
EST:     TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|87027441|gb|CI272206.1|CI272206
EST:     TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGCCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
EST: gi|88902099|gb|CI374707.1|CI374707
EST:     TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCT                         GGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT
genomic: TTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCT

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), 68 (downstream exon)
Score: 34

TTCACAGGCTGCTGAACAAACTGTTGATGAAACTAGCGTTCAAACTCTTGTTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatct ... aatgtgatagGGTGGAAATATCGAGAGAGCAACAGACTGGATTTTTAGCCACCCTGAGGCTTTTAGCTCAGTACCTACTGATTCTTCAACAAGCAATATGGAAGATGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACAGGCTGCTGAACAAACTGTTGATGAAACTAGCGTTCAAACTCTTGTTTCCTTCGGATTTCAAGAAGATGTTGCTCGAAAGGCCTTGGCAGCTTCTgtaataatcttctgtttttaatttcatccatgatagttgatcttttacattttcttgtacagttcgcaatgttgaatacctctcagaaagttgatatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT