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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgggccagtgatttgcttttttatgtgagatatcacactagcatctcctctgcctacatgttcaattgagacctaacaattttgaacttgctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCTGAAACATGGGGCATCCTATTCATCCTCACAATGTATGCTTGTACAACTA

Basic information

species Oryza sativa
transcript LOC_Os08g39420.1
intron # 10
splice site 3'
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|88846577|gb|CI373345.1|CI373345
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88224122|gb|CI223971.1|CI223971
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88835296|gb|CI370599.1|CI370599
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88296760|gb|CI540112.1|CI540112
EST:     TNCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|86853962|gb|CI329408.1|CI329408
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|15858529|gb|BI811341.1|BI811341
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAAC-AACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|86879940|gb|CI340002.1|CI340002
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|89174503|gb|CI110701.1|CI110701
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|88846107|gb|CI372875.1|CI372875
EST:     TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACTAGAGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: TGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
EST: gi|66916970|gb|CX103818.1|CX103818
EST:     AGAGTAACAAACA                         GATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT
genomic: AGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCT

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: 55 (upstream exon), 69 (downstream exon)
Score: 4

ATATTGCGCTTGTAAAGAACAATGCTCTTGTTGGTGCTAAAATTGCTGTGGCCCTTTCTGATCTTCACCAGAGAGTAACAAACAgtaaggttct ... gctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCTGAAACATGGGGCATCCTATTCATCCTCACAATGTATGCTTGTACAACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctctgcctacatgttcaattgagacctaacaattttgaacttgctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCTGAAACATGGGGCATCCTATTCATCCTCACAATGTATGCTTGTACAACTA
                          acctaac  putative branch site (score: 4)
                             taacaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgggccagtgatttgcttttttatgtgagatatcacactagcatctcctctgcctacatgttcaattgagacctaacaattttgaacttgctgtaacagGATTTCGGAGGTCTGCCTTATAGAGTGCATGTACAAAGGCAAGCGAGGTCTGAAACATGGGGCATCCTATTCATCCTCACAATGTATGCTTGTACAACTA

ctgggcc
- - - - - - - tgctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc